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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/MANIFEST.in b/MANIFEST.in index fc709b3..9a07580 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,7 +1,8 @@ include LICENSE include MANIFEST.in -include README.rst +include README.md include setup.py -include run.py +recursive-include variantapi/test *.csv +recursive-include variantapi/test *.vcf recursive-exclude * __pycache__ recursive-exclude * *.py[co] \ No newline at end of file diff --git a/README.md b/README.md index 35e2ed9..7b0ca89 100644 --- a/README.md +++ b/README.md @@ -1,82 +1,223 @@ -# Variant API Client +# VarSome API Client -## A basic api client implementation for [api.varsome.com](https://api.varsome.com) +## A basic API client implementation for [api.varsome.com](https://api.varsome.com) -This client is still in beta but it is a good start to start playing around with the API. +This client is still in beta but it is a good for playing around with the API. + +### Python versions +Requires at least Python 3.3, you can download the latest version from [www.python.org](http://www.python.org) ### Installation +We suggest that you create a python virtual environment instead of globally installing the library. -Either download clone the repository from github and place the variantapi package -within your code, or do +There are several ways to create a virtual environment, but you can refer to [pip installation](https://pip.pypa.io/en/stable/installing/) and +[virtualenv installation](https://virtualenv.pypa.io/en/stable/installation/) to first install these 2 tools if you don't +have them already installed via a package manager (Linux) or HomeBrew (MacOS), etc. +Remember to use "sudo -H" when installing on Mac. - pip install https://github.com/saphetor/variant-api-client-python/archive/master.zip +To create a virtual environment, you can follow the [user guide](https://virtualenv.pypa.io/en/stable/userguide/) or simply run: -### API Documentation + virtualenv -p path_to/python3 venv_dir_name + +Activate the virtual environment: -Please visit the [api documentation](http://docs.varsome.apiary.io) to find out how to use the api and -what values does the api provide as a response to lookup requests + source venv_dir_name/bin/activate -### How to get an API key -You generally are not required to have an api key to use the api, though the number of requests you will be able -to issue will be throttled if they exceed a certain number. +Finally, to use the client, either download or clone the repository from github and place the `varsome_api` +folder inside your project's directory, or run: -Without an API key you will not be able to perform batch requests as well. + pip install https://github.com/saphetor/varsome-api-client-python/archive/master.zip -To obtain an API key please [contact us](mailto:support@saphetor.com) +The client will be installed within your virtual environment. Also, 2 scripts called `varsome_api_run.py` and +`varsome_api_annotate_vcf.py` will be available within your virtual environment's `$PATH`. -### Using the client in your code +### Using the scripts to directly annotate a list of variants or a VCF file + +#### Annotating a variant or list of variants +Try the following query to annotate a single variant: -Using the api client is quite straightforward. Just install the api client package and from within -your code use + varsome_api_run.py -g hg19 -q 'chr7-140453136-A-T' -p add-all-data=1 - from variantapi.client import VariantAPIClient - # api key is not required for single variant lookups - api_key = 'Your token' - api = VariantAPIClient(api_key) - # if you don't have an api key use - # api = VariantAPIClient() - # fetch information about a variant into a dictionary - result = api.lookup('chr19:20082943:1:G', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19') - # access results e.g. the transcripts of the variant - transcripts = result['refseq_transcripts'] - # fetch information for multiple variants - variants = ['chr19:20082943:1:G','chr22:39777823::CAA'] - # results will be an array of dictionaries an api key will be required for this request - results = api.batch_lookup(variants, params={'add-source-databases': 'gnomad-exomes,gnomad-genomes'}, ref_genome='hg19') +The script should complete without errors and display aproximately 6,700 lines of data from `dann`, `dbnsfp`, `ensembl_transcripts`, `gerp`, `gnomad_exomes`, `gnomad_exomes_coverage`, `icgc_somatic`, `ncbi_clinvar2`, `pub_med_articles`, `refseq_transcripts`, `sanger_cosmic_public`, `uniprot_variants`, `wustl_civic` etc. +The script can also accept a text file with variants (one per line) and an optional output file to store the +annotations in. We suggest that you don't use this script for a large number of variants, but use +the client within your code instead. -If errors occur while using the client an exception will be thrown. -You may wish to catch this exception and proceed with your own code logic + varsome_api_run.py -g hg19 -k api_key -i variants.txt -o annotations.txt -p add-all-data=1 + +The command above will read variants from `variants.txt` and dump the annotations to `annotations.txt`. +For any substantial number of variants you will need to register for an API key. You can try the software without +the -k apiKey parameter but you will quickly get an HTTP status code 429 (too many requests) error. - from variantapi.client import VariantAPIClient, VariantApiException - api = VariantAPIClient() - try: - result = api.lookup('chr19:20082943:1:G', ref_genome='hg64') - except VariantApiException as e: - # proceed with your code flow e.g. - print(e) # 404 (invalid reference genome) +#### Annotating a VCF file +To annotate a VCF file, use: -### Example Usage + varsome_api_annotate_vcf.py -g hg19 -k api_key -i input.vcf -o annotated_vcf.vcf -p add-all-data=1 + +Notice, however, that not all available annotations will be present in the `annotated_vcf.vcf` file. Only a subset +of the returned annotations will be available when running this script. See the "Using the client in your code" +section below for how to annotate a VCF file with the annotations that are of interest to you. +### Using the client in your code + +Using the API client is quite straightforward. Just install the API client package and use the following in your code: +```python +from varsome_api.client import VarSomeAPIClient +# API key is not required for single variant lookups +api_key = 'Your token' +api = VarSomeAPIClient(api_key) +# if you don't have an API key use +# api = VarSomeAPIClient() +# fetch information about a variant into a dictionary +result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19') +# access results e.g. the transcripts of the variant +transcripts = result['refseq_transcripts'] +# fetch information for multiple variants +variants = ['chr19:20082943:1:G','chr22:39777823::CAA'] +# Results will be an array of dictionaries. An API key will be required for this request +results = api.batch_lookup(variants, params={'add-source-databases': 'gnomad-exomes,gnomad-genomes'}, ref_genome='hg19') +# look at the python doc for batch_lookup method for additional parameters +``` +If errors occur while using the client, an exception will be thrown. +You may wish to catch this exception and proceed with your own code logic: + +```python +from varsome_api.client import VarSomeAPIClient, VarSomeAPIException +api = VarSomeAPIClient() +try: + result = api.lookup('chr19:20082943:1:G', ref_genome='hg64') +except VarSomeAPIException as e: + # proceed with your code flow e.g. + print(e) # 404 (invalid reference genome) +``` + +To view available request parameters (used by the `params` method parameter), refer to an example at [api.varsome.com](https://api.varsome.com). + +To understand how annotation properties are included in the JSON response, please refer to the relevant [schema](https://api.varsome.com/lookup/schema). + +#### JSON response wrapper + +If you don't want to read through each attribute in the JSON response, you can wrap the result into a Python +[JSON model](http://jsonmodels.readthedocs.io/en/latest/readme.html): + +```python +from varsome_api.client import VarSomeAPIClient +from varsome_api.models.variant import AnnotatedVariant +# API key is not required for single variant lookups +api_key = 'Your token' +api = VarSomeAPIClient(api_key) +# fetch information about a variant into a dictionary +result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19') +annotated_variant = AnnotatedVariant(**result) +``` + +You now have access to a set of shortcut attributes (these will be updated over time in the code base): + +```python +annotated_variant.chromosome +annotated_variant.alt +annotated_variant.genes # directly get the genes related to the variant +annotated_variant.gnomad_exomes_af # etc +``` +Or you may access other inner properties of other available properties: + +```python +# get gnomad exomes allele number +allele_number = [gnomad_exome.an for gnomad_exome in annotated_variant.gnomad_exomes] +``` + +JSON model-type objects that contain a `version` property, like `annotated_variant.gnomad_exomes`, are +always returned as lists of objects. This is because the API has the ability to return multiple versions of +annotation databases (although this is not currently publicly available). For consistency, therefore, +these are always lists, though it is safe to assume that they will only include a single item. So it is safe +to rewrite as: + +```python +try: + allele_number = [gnomad_exome.an for gnomad_exome in annotated_variant.gnomad_exomes][0] +except IndexError: + pass # no gnomad exomes annotation for the variant +``` + +#### Annotating a VCF using the client + +To annotate a VCF you can base your code on the VCFAnnotator object. This provides a basic implementation that +will annotate a VCF file using a set of the available annotations. It uses [PyVCF](https://github.com/jamescasbon/PyVCF) to read and write to VCF files. + +```python +from varsome_api.vcf import VCFAnnotator +api_key = 'Your token' +vcf_annotator = VCFAnnotator(api_key=api_key, ref_genome='hg19', get_parameters={'add-all-data': 1, 'expand-pubmed-articles': 0}) +vcf_file = 'input.vcf' +output_vcf_file = 'annotated.vcf' +vcf_annotator.annotate(vcf_file, output_vcf_file) +``` + +To annotate the VCF file with the annotations that you are interested in, you need only override 2 methods +(`annotate_record` and `add_vcf_header_info`) in the VCFAnnotator class: + +```python +from varsome_api.vcf import VCFAnnotator +from vcf.parser import _Info +class MyVCFAnnotator(VCFAnnotator): + + def annotate_record(self, record, variant_result): + """ + :param record: vcf record object + :param variant_result: AnnotatedVariant object + :return: annotated record object + """ + record.INFO['gnomad_exomes_AN'] = variant_result.gnomad_exomes_an + # if you wish to also include the default annotations + # return super().annotate_record(record, variant_result) + return record + + + def add_vcf_header_info(self, vcf_template): + """ + Adds vcf INFO headers for the annotated values provided + :param vcf_template: vcf reader object + :return: + """ + vcf_template.infos['gnomad_exomes_AN'] = _Info('gnomad_exomes_AN', '.', 'Integer', + 'GnomAD exomes allele number value', None, None) + # if you wish to also include the default headers + # super().add_vcf_header_info(vcf_template) + +api_key = 'Your token' +vcf_annotator = MyVCFAnnotator(api_key=api_key, ref_genome='hg19', get_parameters={'add-all-data': 1, 'expand-pubmed-articles': 0}) +vcf_file = 'input.vcf' +output_vcf_file = 'annotated.vcf' +vcf_annotator.annotate(vcf_file, output_vcf_file) +``` + +### API Documentation -You may download and run the run.py python file after installation of the package -to test the api client directly e.g. +See [API documentation](https://api.varsome.com) for information on how to use the API and +what values the API provides as a response to lookup requests. + +### How to get an API key - ./run.py -g hg19 -q 'chr19:20082943:1:G' -p add-all-data=1 +To obtain an API key please [contact us](mailto:support@saphetor.com). -You may pass more than one values after the -q argument that will make a batch request -to the API but you will need a token to do that e.g. +You can use the API without an API key, but performance and the number of queries will be +limited in order to safeguard our platform's reliability. - ./run.py -k 'your token' -g hg19 -q 'rs113488022' 'chr19:20082943:1:G' -p add-source-databases=gnomad-exomes,gnomad-genomes +You will also not be able to perform batch requests without an API key. -Run - ./run.py -h +### How to run the tests -for a list of available options +Clone the repository, after creating a virtual environment, and run: -To view available request parameters (used in the params method parameter) refer to an example at [api.varsome.com](https://api.varsome.com) or -the [api documentation](http://docs.varsome.apiary.io). + python setup.py test + +Running the tests will install [nose](https://nose.readthedocs.io/en/latest/) in your virtual environment. +To run the tests, set the `VARSOME_API_KEY` environment variable to your API token. Otherwise, +several tests will fail because the API will return a 429 (too many requests) or 401 (not authenticated) error. +Be advised as well that running the tests will count towards your account request limit depending on the +API package you are subscribed to. + -To understand how annotation properties are included in the json response please refer to the relevant [schema](https://api.varsome.com/lookup/schema) diff --git a/batchRequestClient.py b/batchRequestClient.py deleted file mode 100644 index 03f7fad..0000000 --- a/batchRequestClient.py +++ /dev/null @@ -1,85 +0,0 @@ -#!/usr/bin/env python3 - -# A simple client application that does the following: -# - Loads a text file containing one variant per row -# - Performs a batch lookups to the Saphetor Variant API using N variants at a time. -# - Saves the results in a new file. -# -# It uses the following module: -# variantapi.client (https://github.com/saphetor/variant-api-client-python) -# -# Note: To sort output json file execute: -# jq -S '.' output.txt > output_sorted.txt - -import argparse -import json -import logging -import re -import sys -import operator -from sys import argv -from variantapi.client import VariantAPIClient - -__author__ = 'stephanos-androutsellis' - -# Declare reference genome as a global variable -_ref_genome = 1019 - - -def main(argv): - # Read and parse arguments - infile = '' - outfile = '' - batch_size = 5000 - - parser = argparse.ArgumentParser(description='Simple batch lookup Client application') - parser.add_argument('-i', help='Input file', type=str, metavar='Input File', required=True) - parser.add_argument('-o', help='Output file', type=str, metavar='Output File', required=True) - parser.add_argument('-n', help="Number of variants to batch", type=int, metavar='Batch size', required=True,default=5000) - parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=False) - parser.add_argument('-g', help='Reference genome either 1019 (default) or 1038', type=int, - metavar='Reference Genome', required=False, default=1019) - - args = parser.parse_args() - infile = args.i - outfile = args.o - batch_size = args.n if args.n is not None else batch_size - api_key = args.k - ref_genome = args.g if args.g is not None else _ref_genome - - # Open and load input file into list - print("Reading input file ", infile) - with open(infile) as fi: - variants = fi.readlines() - variants = [v.strip('\n') for v in variants] - - # Prepare output for writing. - print("Opening output file ", outfile) - fo = open(outfile,'w') - - # Initialize client connection to API - api = VariantAPIClient(api_key) - if (api is None): - print("Failed to connect to API") - sys.exit() - - batch_counter = 0 - finished = False - while not finished: - start_index = batch_counter*batch_size - end_index = (batch_counter+1)*batch_size - if (end_index > len(variants)): - end_index = len(variants) - finished = True - print(start_index, ":", end_index-1) - batch_variants = variants[start_index:end_index] - print("Lookup for: ", batch_variants, "with ref_genome= ", ref_genome) - batch_data = api.batch_lookup(batch_variants, ref_genome=ref_genome) - - fo.write(json.dumps(batch_data, indent=2)) - batch_counter += 1 - - print ("Finished ", batch_counter, " batch lookups") - -if __name__ == '__main__': - main(argv) diff --git a/output.vcf b/output.vcf deleted file mode 100644 index eba086a..0000000 --- a/output.vcf +++ /dev/null @@ -1,2133 +0,0 @@ -##fileformat=VCFv4.1 -##GATKCommandLine= -##GATKCommandLine= -##GATKCommandLine= -##reference=file:///ref/genomes/hg19/hg19.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##contig= 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-##contig= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR309291 -chr6 44387517 rs6923521 C G 184.84 PASS AC=2;AF=1.0;AN=2;DB;DP=6;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.81;SOR=3.912;VQSLOD=6.47;culprit=FS;GENE=CDC5L GT:AD:DP:GQ:PL 1/1:0,6:6:18:213,18,0 -chr6 44410746 rs61581947 GT G 17.78 LowQual AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=5.93;SOR=2.303;GENE=CDC5L GT:AD:DP:GQ:PL 1/1:0,2:2:6:54,6,0 -chr6 44453701 rs60176543 G A 15.65 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=7.83;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0 -chr6 44505655 rs9296442 G T 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 -chr6 44526440 rs991234 A C 36.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.37;SOR=0.693;VQSLOD=7.54;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:64,6,0 -chr6 44532454 rs76750540 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44547060 rs67452991 C T 102.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.51;SOR=0.693;VQSLOD=5.66;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:130,12,0 -chr6 44562107 rs491616 G C 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:28:40,0,28 -chr6 44575012 rs636287 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44584484 rs634631 A T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44585311 rs648579 T C 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.91;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 44586011 rs651831 G C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44586363 rs6913259 C T 171.9 PASS AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.38;SOR=3.611;VQSLOD=6.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:200,15,0 -chr6 44595393 rs1767788 C T 53.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=9.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 44605066 rs6934182 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44605461 rs4714809 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44629576 rs4257850 A G 60.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=2.303;VQSLOD=9.47;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:88,6,0 -chr6 44635852 rs4711794 C A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44640206 rs527082 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44775098 . C A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44780682 rs622923 G T 14.68 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=7.34;SOR=1.609;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,1:1:3:41,3,0 -chr6 44780701 rs559322 C T 15.65 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=7.83;SOR=1.609;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0 -chr6 44781313 rs5875893 G GA 15.82 LowQual AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=3.95;SOR=2.303;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:52,6,0 -chr6 44797271 rs9369514 C A 241.8 PASS AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.54;SOR=2.584;VQSLOD=6.76;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,7:7:21:270,21,0 -chr6 44825715 rs9395051 C A 71.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.76;SOR=0.693;VQSLOD=7.41;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 -chr6 44834094 rs3846896 G A 15.65 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=7.83;SOR=1.609;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0 -chr6 44840376 rs1293588 A C 40.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=20.37;SOR=2.303;VQSLOD=6.79;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 44888740 rs608941 C T 94.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=1.179;VQSLOD=8.87;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,3:3:9:122,9,0 -chr6 44899632 rs679713 T C 1144.77 PASS AC=2;AF=1.0;AN=2;DB;DP=27;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.54;SOR=6.666;VQSLOD=6.85;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,27:27:81:1173,81,0 -chr6 44900253 rs3799986 A G 188.9 PASS AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.64;SOR=3.611;VQSLOD=6.39;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,5:5:15:217,15,0 -chr6 44903248 rs10948186 C T 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=2.303;VQSLOD=8.97;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 44921320 rs10948187 C T 89.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.76;SOR=2.833;VQSLOD=8.75;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,3:3:9:117,9,0 -chr6 44921962 rs625782 T C 65.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.76;SOR=2.833;VQSLOD=7.9;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,3:3:9:93,9,0 -chr6 44935341 rs636845 C T 60.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.09;SOR=1.179;VQSLOD=8.15;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,3:3:9:88,9,0 -chr6 44952716 rs5875900 GT G 29.71 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=14.85;SOR=0.693;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:66,6,0 -chr6 44972729 rs1159132 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44988149 rs1475534 C T 529.77 PASS AC=2;AF=1.0;AN=2;DB;DP=14;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.74;SOR=5.421;VQSLOD=7.17;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,14:14:42:558,42,0 -chr6 45003928 rs4398713 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45020697 rs2149872 A G 61.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.4;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 -chr6 45066168 rs150556986 G A 167.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.388;ClippingRankSum=0.194;DB;DP=14;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.194;POSITIVE_TRAIN_SITE;QD=11.98;ReadPosRankSum=-0.968;SOR=1.402;VQSLOD=5.5;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 0/1:8,6:14:99:196,0,294 -chr6 45073967 rs2396381 A G 88.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.43;SOR=2.833;VQSLOD=8.42;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,3:3:9:116,9,0 -chr6 45090876 . T C 19.79 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=9.89;SOR=0.693;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:47,6,0 -chr6 45159414 rs11321900 TA T 24.72 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=12.36;SOR=0.693;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 -chr6 45163350 rs1748242 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45170121 rs1284955 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45175908 rs9381373 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45177025 rs2396425 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45192941 rs6911320 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45203918 rs6937317 T C 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.23;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 45268574 rs111541141 T TAAGAC 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.28;culprit=FS;GENE=SUPT3H GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 45360194 rs9395099 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RUNX2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45390962 rs11498196 C T 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=7.55;culprit=FS;GENE=RUNX2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 45444061 rs2677110 C T 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=9.1;culprit=FS;GENE=RUNX2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 45444083 rs35663521 G GA 38.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=0.693;VQSLOD=7.75;culprit=FS;GENE=RUNX2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 45456564 rs12215249 G T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RUNX2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45486207 rs7771889 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RUNX2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45511541 rs10948238 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RUNX2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45519443 . A G 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RUNX2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45521733 rs1201807 C T 47.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=2.303;VQSLOD=8.89;culprit=FS;GENE=RUNX2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 45521847 rs70996341 ATGTG A 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=5.79;culprit=FS;GENE=RUNX2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 45523928 rs675613 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RUNX2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45523947 rs5875926 G GA 24.72 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=12.36;SOR=0.693;GENE=RUNX2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 -chr6 45564510 rs713270 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RUNX2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45609347 . G GT 22.73 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=11.36;SOR=0.693;GENE=RUNX2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:59,6,0 -chr6 45705659 rs829913 T A 96.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.09;SOR=1.179;VQSLOD=7.64;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:124,9,0 -chr6 45733276 rs6942337 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45749983 rs9357491 A G 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.52;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 45754997 rs1037281 A C 50.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=0.693;VQSLOD=9.52;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 45764956 rs11276783 ACAGGGCAGCT A 98.25 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.75;SOR=2.833;VQSLOD=7.83;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 45769869 rs10948257 G A 49.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=7.93;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 45792170 rs12197564 G T 13.72 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=6.86;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 -chr6 45808216 . C A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45833836 rs142466444 TTTTC T 85.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=-0.727;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.727;POSITIVE_TRAIN_SITE;QD=17.15;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=6.32;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:43:123,0,43 -chr6 45847678 rs2396559 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45851886 rs1932042 C T 61.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.58;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 -chr6 45858548 rs71566550 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45870999 rs35735653 CAG C 269.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.065;ClippingRankSum=0.457;DB;DP=33;FS=4.212;MLEAC=1;MLEAF=0.5;MQ=59.43;MQ0=0;MQRankSum=-1.588;POSITIVE_TRAIN_SITE;QD=8.17;ReadPosRankSum=0.239;SOR=1.802;VQSLOD=2.22;culprit=FS;GENE=CLIC5 GT:AD:DP:GQ:PL 0/1:22,9:31:99:307,0,882 -chr6 45888576 rs34155361 ATGC A 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.66;culprit=FS;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 45893031 rs6939554 C T 35.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.87;SOR=0.693;VQSLOD=7.73;culprit=FS;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:63,6,0 -chr6 45901916 rs9349337 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45909139 rs11421773 C CG 234.74 PASS AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.08;SOR=2.833;VQSLOD=6.34;culprit=FS;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,8:8:27:272,27,0 -chr6 45914028 rs3777582 A T 13.72 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=13.72;SOR=1.609;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 -chr6 45915413 rs1890368 C G 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.11;culprit=FS;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 45915504 rs1890369 A C 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.66;culprit=FS;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 45919719 rs3777587 A G 60.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=2.303;VQSLOD=6.51;culprit=FS;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:88,6,0 -chr6 45919758 rs3777588 G A 120.78 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.731;ClippingRankSum=-0.731;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.731;POSITIVE_TRAIN_SITE;QD=24.16;ReadPosRankSum=0.731;SOR=1.981;VQSLOD=6.26;culprit=FS;GENE=CLIC5 GT:AD:DP:GQ:PL 0/1:1,4:5:27:149,0,27 -chr6 45921108 rs3777590 G C 63.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=9.08;culprit=FS;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 45922849 rs3734206 C T 1890.77 PASS AC=2;AF=1.0;AN=2;DB;DP=48;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.58;SOR=6.316;VQSLOD=6.34;culprit=QD;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,47:47:99:1919,141,0 -chr6 45923126 rs6909306 A C 252.78 PASS AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.6;SOR=4.407;VQSLOD=6.96;culprit=FS;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,8:8:24:281,24,0 -chr6 45965608 rs3777612 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45989366 rs1204338 A C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45994992 rs1547605 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46025834 rs1535110 T G 23.58 LowQual AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=7.86;SOR=0.693;GENE=CLIC5 GT:AD:DP:GQ:PL 1/1:0,2:2:7:51,7,0 -chr6 46047269 rs9381423 T C 124.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.945;ClippingRankSum=0.453;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.55;MQ0=0;MQRankSum=-1.586;POSITIVE_TRAIN_SITE;QD=7.8;ReadPosRankSum=1.586;SOR=0.223;VQSLOD=4.04;culprit=QD;GENE=CLIC5 GT:AD:DP:GQ:PL 0/1:11,5:16:99:153,0,375 -chr6 46047458 rs3734207 C T 3075.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-7.19;ClippingRankSum=-0.231;DB;DP=213;FS=0.542;MLEAC=1;MLEAF=0.5;MQ=59.59;MQ0=0;MQRankSum=-1.583;POSITIVE_TRAIN_SITE;QD=14.44;ReadPosRankSum=0.457;SOR=0.754;VQSLOD=1.68;culprit=FS;GENE=CLIC5 GT:AD:DP:GQ:PL 0/1:107,105:212:99:3104,0,3533 -chr6 46048000 rs1416165 T C 2778.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.171;ClippingRankSum=0.218;DB;DP=172;FS=0.639;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.131;POSITIVE_TRAIN_SITE;QD=16.16;ReadPosRankSum=-1.044;SOR=0.794;VQSLOD=1.61;culprit=FS;GENE=CLIC5 GT:AD:DP:GQ:PL 0/1:74,98:172:99:2807,0,2169 -chr6 46107115 rs61381984 A AT 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=4;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=3.01;ReadPosRankSum=0.736;SOR=2.225;GENE=ENPP4 GT:AD:DP:GQ:PL 0/1:1,2:3:20:49,0,20 -chr6 46107312 rs11752816 G A 1890.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.79;ClippingRankSum=0.077;DB;DP=125;FS=3.508;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.58;POSITIVE_TRAIN_SITE;QD=15.13;ReadPosRankSum=-1.351;SOR=0.335;VQSLOD=2.14;culprit=ReadPosRankSum;GENE=ENPP4 GT:AD:DP:GQ:PL 0/1:62,63:125:99:1919,0,1762 -chr6 46107752 rs7451713 C G 5119.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=7.032;ClippingRankSum=-2.826;DB;DP=301;FS=1.419;MLEAC=1;MLEAF=0.5;MQ=59.92;MQ0=0;MQRankSum=-0.805;POSITIVE_TRAIN_SITE;QD=17.01;ReadPosRankSum=0.708;SOR=0.792;VQSLOD=1.55;culprit=DP;GENE=ENPP4 GT:AD:DP:GQ:PL 0/1:146,155:301:99:5148,0,4240 -chr6 46110821 rs7769902 A G 202.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.085;ClippingRankSum=0.38;DB;DP=19;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.78;MQ0=0;MQRankSum=-0.211;POSITIVE_TRAIN_SITE;QD=10.67;ReadPosRankSum=-0.549;SOR=0.321;VQSLOD=4.71;culprit=FS;GENE=ENPP4 GT:AD:DP:GQ:PL 0/1:12,7:19:99:231,0,378 -chr6 46110844 rs35942390 T TGA 174.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.717;ClippingRankSum=-0.444;DB;DP=27;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.95;MQ0=0;MQRankSum=1.467;POSITIVE_TRAIN_SITE;QD=6.47;ReadPosRankSum=-0.853;SOR=0.307;VQSLOD=5.69;culprit=FS;GENE=ENPP4 GT:AD:DP:GQ:PL 0/1:14,8:22:99:212,0,429 -chr6 46124799 rs9367237 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46129345 rs2235881 G A 4707.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=6.532;ClippingRankSum=-0.307;DB;DP=317;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.01;MQ0=0;MQRankSum=0.655;POSITIVE_TRAIN_SITE;QD=14.85;ReadPosRankSum=2.066;SOR=0.698;VQSLOD=1.89;culprit=FS;GENE=ENPP5 GT:AD:DP:GQ:PL 0/1:162,154:316:99:4736,0,4689 -chr6 46135489 rs6926570 T C 3065.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=6.245;ClippingRankSum=0.018;DB;DP=187;FS=1.135;MLEAC=1;MLEAF=0.5;MQ=59.75;MQ0=0;MQRankSum=0.009;POSITIVE_TRAIN_SITE;QD=16.39;ReadPosRankSum=1.61;SOR=0.809;VQSLOD=2.66;culprit=DP;GENE=ENPP5 GT:AD:DP:GQ:PL 0/1:96,91:187:99:3094,0,2997 -chr6 46135984 rs3806995 G T 1685.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.855;ClippingRankSum=-0.003;DB;DP=117;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.406;POSITIVE_TRAIN_SITE;QD=14.41;ReadPosRankSum=2.665;SOR=0.727;VQSLOD=4.05;culprit=FS;GENE=ENPP5 GT:AD:DP:GQ:PL 0/1:61,56:117:99:1714,0,1985 -chr6 46148778 rs34512199 AT A 24.72 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=12.36;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 -chr6 46170924 . G T 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46206776 rs55832349 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RCAN2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46219283 rs6910477 G A 47.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=2.303;VQSLOD=8.19;culprit=FS;GENE=RCAN2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 46259017 rs11389800 G GT 13.89 LowQual AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=63.51;MQ0=0;QD=4.63;SOR=2.303;GENE=RCAN2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:50,6,0 -chr6 46293328 rs2277121 G A 717.77 PASS AC=2;AF=1.0;AN=2;DB;DP=19;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.88;SOR=5.994;VQSLOD=6.73;culprit=FS;GENE=RCAN2 GT:AD:DP:GQ:PL 1/1:0,19:19:57:746,57,0 -chr6 46296710 rs6906742 C T 62.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.44;culprit=FS;GENE=RCAN2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 46302975 rs60870663 T A 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.4;culprit=FS;GENE=RCAN2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 46302987 rs58585138 A G 46.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.37;SOR=2.303;VQSLOD=7.24;culprit=FS;GENE=RCAN2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:74,6,0 -chr6 46312875 rs9367242 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RCAN2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46321514 . T C 20.78 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.39;SOR=0.693;GENE=RCAN2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:48,6,0 -chr6 46326865 . C G 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=RCAN2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46456536 rs9349362 C T 33.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=11.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=5.66;culprit=FS;GENE=RCAN2 GT:AD:DP:GQ:PL 0/1:1,2:3:34:62,0,34 -chr6 46462514 . C A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46469927 rs59470467 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46470622 rs67200907 G A 48.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.76;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 46479322 rs1609661 A G 63.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.22;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 46490097 rs4714943 C A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46512200 . T C 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46521602 rs699939 C A 599.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.64;ClippingRankSum=0.714;DB;DP=46;FS=1.296;MLEAC=1;MLEAF=0.5;MQ=59.5;MQ0=0;MQRankSum=-0.647;POSITIVE_TRAIN_SITE;QD=13.04;ReadPosRankSum=2.186;SOR=0.911;VQSLOD=2.11;culprit=ReadPosRankSum;GENE=CYP39A1 GT:AD:DP:GQ:PL 0/1:27,19:46:99:628,0,724 -chr6 46563817 rs7761731 A T 3102.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.173;ClippingRankSum=-1.345;DB;DP=194;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.76;MQ0=0;MQRankSum=0.519;POSITIVE_TRAIN_SITE;QD=15.99;ReadPosRankSum=0.699;SOR=0.739;VQSLOD=2.35;culprit=FS;GENE=CYP39A1 GT:AD:DP:GQ:PL 0/1:90,104:194:99:3131,0,2802 -chr6 46607081 rs3085602 AT A 645.73 PASS AC=2;AF=1.0;AN=2;DB;DP=20;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.29;SOR=6.091;VQSLOD=5.95;culprit=FS;GENE=CYP39A1 GT:AD:DP:GQ:PL 1/1:0,20:20:60:683,60,0 -chr6 46620252 rs12192544 C G 5715.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=2.691;ClippingRankSum=0.485;DB;DP=440;FS=1.133;MLEAC=1;MLEAF=0.5;MQ=59.75;MQ0=0;MQRankSum=-2.934;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=12.99;ReadPosRankSum=-0.818;SOR=0.805;VQSLOD=-0.9355;culprit=MQRankSum;GENE=CYP39A1,SLC25A27 GT:AD:DP:GQ:PL 0/1:239,200:439:99:5744,0,6851 -chr6 46623698 rs3757241 T C 6720.77 PASS AC=2;AF=1.0;AN=2;DB;DP=183;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.06;SOR=0.822;VQSLOD=5.03;culprit=FS;GENE=SLC25A27 GT:AD:DP:GQ:PL 1/1:0,179:179:99:6749,538,0 -chr6 46625274 rs9381468 A G 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=9.35;culprit=DP;GENE=SLC25A27 GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 46626353 rs953062 A G 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.6;culprit=FS;GENE=SLC25A27 GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 46630068 rs9381469 G A 907.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.991;ClippingRankSum=-0.318;DB;DP=68;FS=14.136;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.231;POSITIVE_TRAIN_SITE;QD=13.35;ReadPosRankSum=1.115;SOR=3.003;VQSLOD=1.21;culprit=FS;GENE=SLC25A27 GT:AD:DP:GQ:PL 0/1:40,28:68:99:936,0,1206 -chr6 46637908 rs200254015 A C 76.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-5.158;ClippingRankSum=-1.074;DB;DP=72;FS=148.77;MLEAC=1;MLEAF=0.5;MQ=59.36;MQ0=0;MQRankSum=-0.756;QD=1.07;ReadPosRankSum=-5.463;SOR=5.781;VQSLOD=-47.45;culprit=FS;GENE=SLC25A27 GT:AD:DP:GQ:PL 0/1:55,17:72:99:105,0,1883 -chr6 46649231 rs7740677 C T 6652.77 PASS AC=2;AF=1.0;AN=2;DB;DP=183;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.24;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.56;SOR=2.067;VQSLOD=5.55;culprit=FS;GENE=TDRD6 GT:AD:DP:GQ:PL 1/1:0,183:183:99:6681,550,0 -chr6 46657057 rs3799277 A G 4300.77 PASS AC=2;AF=1.0;AN=2;DB;DP=112;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.78;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.29;SOR=1.35;VQSLOD=6.24;culprit=FS;GENE=TDRD6 GT:AD:DP:GQ:PL 1/1:0,111:111:99:4329,334,0 -chr6 46658905 rs9381472 C G 2370.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.957;ClippingRankSum=-1.243;DB;DP=147;FS=3.996;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.165;POSITIVE_TRAIN_SITE;QD=16.13;ReadPosRankSum=0.979;SOR=1.036;VQSLOD=2.15;culprit=DP;GENE=TDRD6 GT:AD:DP:GQ:PL 0/1:77,70:147:99:2399,0,2735 -chr6 46661937 rs55724083 CT C 307.76 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.021;ClippingRankSum=0.615;DB;DP=81;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.11;MQ0=0;MQRankSum=-0.913;POSITIVE_TRAIN_SITE;QD=3.8;ReadPosRankSum=0.542;SOR=3.026;VQSLOD=5.76;culprit=FS;GENE=TDRD6 GT:AD:DP:GQ:PL 0/1:6,30:36:22:345,0,22 -chr6 46672205 . TCTCTCTCTCTCA T 62.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.219;ClippingRankSum=0.361;DP=48;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.85;MQ0=0;MQRankSum=-1.307;QD=1.31;ReadPosRankSum=2.219;SOR=0.892;VQSLOD=2.56;culprit=FS;GENE=TDRD6,PLA2G7 GT:AD:DP:GQ:PL 0/1:15,5:20:99:100,0,440 -chr6 46672452 rs148052037 TAATC T 1973.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.65;ClippingRankSum=1.355;DB;DP=107;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.1;MQ0=0;MQRankSum=-2.444;POSITIVE_TRAIN_SITE;QD=18.45;ReadPosRankSum=-0.854;SOR=0.718;VQSLOD=3.96;culprit=FS;GENE=TDRD6,PLA2G7 GT:AD:DP:GQ:PL 0/1:51,52:103:99:2011,0,3030 -chr6 46672943 rs1051931 A G 6548.77 PASS AC=2;AF=1.0;AN=2;DB;DP=172;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.65;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.43;SOR=1.172;VQSLOD=3.94;culprit=FS;GENE=PLA2G7 GT:AD:DP:GQ:PL 1/1:0,170:170:99:6577,511,0 -chr6 46676019 rs2216465 C G 430.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.311;ClippingRankSum=0.241;DB;DP=29;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.548;POSITIVE_TRAIN_SITE;QD=14.85;ReadPosRankSum=-0.022;SOR=0.518;VQSLOD=5.37;culprit=FS;GENE=PLA2G7 GT:AD:DP:GQ:PL 0/1:16,13:29:99:459,0,615 -chr6 46682079 rs1362931 A C 1919.77 PASS AC=2;AF=1.0;AN=2;DB;DP=50;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.23;SOR=7.864;VQSLOD=7.44;culprit=FS;GENE=PLA2G7 GT:AD:DP:GQ:PL 1/1:0,50:50:99:1948,150,0 -chr6 46683978 rs41361844 T TA 363.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.549;ClippingRankSum=1.214;DB;DP=33;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.33;MQ0=0;MQRankSum=-0.419;POSITIVE_TRAIN_SITE;QD=11.02;ReadPosRankSum=1.046;SOR=0.473;VQSLOD=6.0;culprit=FS;GENE=PLA2G7 GT:AD:DP:GQ:PL 0/1:17,13:30:99:401,0,436 -chr6 46684222 rs1805017 C T 2595.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.964;ClippingRankSum=-0.355;DB;DP=171;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.76;MQ0=0;MQRankSum=1.275;POSITIVE_TRAIN_SITE;QD=15.18;ReadPosRankSum=0.601;SOR=0.648;VQSLOD=2.6;culprit=FS;GENE=PLA2G7 GT:AD:DP:GQ:PL 0/1:85,85:170:99:2624,0,2396 -chr6 46685286 rs6929105 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PLA2G7 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46689762 rs9472830 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PLA2G7 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46695144 . G A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PLA2G7 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46714081 rs141667902 GTTCTCC G 187.87 PASS AC=2;AF=1.0;AN=2;DB;DP=6;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=48.03;MQ0=0;QD=31.31;SOR=1.022;VQSLOD=5.89;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:225,15,0 -chr6 46727772 rs6918050 G C 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.87;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 46730039 . A G 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=27.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46761495 rs2274656 G A 1258.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.705;ClippingRankSum=0.492;DB;DP=66;FS=11.133;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.161;POSITIVE_TRAIN_SITE;QD=19.07;ReadPosRankSum=0.794;SOR=0.077;VQSLOD=0.934;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:26,40:66:99:1287,0,859 -chr6 46766467 rs872018 G C 826.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.434;ClippingRankSum=0.387;DB;DP=45;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.49;MQ0=0;MQRankSum=0.716;POSITIVE_TRAIN_SITE;QD=18.37;ReadPosRankSum=-3.462;SOR=1.681;VQSLOD=3.22;culprit=ReadPosRankSum;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:22,22:44:99:855,0,1647 -chr6 46766468 rs872019 G C 826.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.555;ClippingRankSum=-0.67;DB;DP=46;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.55;MQ0=0;MQRankSum=-0.329;POSITIVE_TRAIN_SITE;QD=17.97;ReadPosRankSum=-2.986;SOR=1.609;VQSLOD=4.2;culprit=ReadPosRankSum;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:23,22:45:99:855,0,1647 -chr6 46775361 rs2894714 A G 95.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.76;SOR=1.179;VQSLOD=6.48;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 1/1:0,3:3:9:123,9,0 -chr6 46777377 rs1833460 T C 2742.77 PASS AC=2;AF=1.0;AN=2;DB;DP=78;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.7;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.37;SOR=5.892;VQSLOD=6.63;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 1/1:0,78:78:99:2771,235,0 -chr6 46784183 rs9367257 A G 59.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.03;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 46793175 rs6920863 G A 976.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.347;ClippingRankSum=0.69;DB;DP=69;FS=2.675;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.762;POSITIVE_TRAIN_SITE;QD=14.16;ReadPosRankSum=-0.654;SOR=0.378;VQSLOD=3.19;culprit=ReadPosRankSum;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:35,34:69:99:1005,0,1233 -chr6 46794048 rs2297018 C G 1559.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.778;ClippingRankSum=1.15;DB;DP=86;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.92;MQ0=0;MQRankSum=0.527;POSITIVE_TRAIN_SITE;QD=18.14;ReadPosRankSum=-0.821;SOR=0.791;VQSLOD=4.49;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:41,45:86:99:1588,0,1376 -chr6 46797329 rs2274657 G A 1320.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.675;ClippingRankSum=0.827;DB;DP=98;FS=1.251;MLEAC=1;MLEAF=0.5;MQ=58.33;MQ0=0;MQRankSum=-0.371;POSITIVE_TRAIN_SITE;QD=13.48;ReadPosRankSum=0.307;SOR=0.399;VQSLOD=3.23;culprit=DP;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:53,45:98:99:1349,0,1847 -chr6 46797515 rs6903045 G A 68.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.406;ClippingRankSum=0.406;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.406;POSITIVE_TRAIN_SITE;QD=11.46;ReadPosRankSum=0.406;SOR=2.093;VQSLOD=6.66;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:3,3:6:73:97,0,73 -chr6 46801071 rs2274658 G T 2458.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.72;ClippingRankSum=0.231;DB;DP=169;FS=2.721;MLEAC=1;MLEAF=0.5;MQ=59.86;MQ0=0;MQRankSum=-0.436;POSITIVE_TRAIN_SITE;QD=14.55;ReadPosRankSum=2.14;SOR=0.917;VQSLOD=2.52;culprit=ReadPosRankSum;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:89,80:169:99:2487,0,2786 -chr6 46802172 . ATATTTATT A 98.25 PASS AC=2;AF=1.0;AN=2;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=32.75;SOR=2.833;VQSLOD=6.56;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 46802370 rs4714952 G A 4383.77 PASS AC=2;AF=1.0;AN=2;DB;DP=119;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.22;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.86;SOR=1.198;VQSLOD=7.13;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 1/1:0,119:119:99:4412,357,0 -chr6 46802901 rs2297021 G C 87.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.72;ClippingRankSum=0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.38;MQ0=0;MQRankSum=0.72;POSITIVE_TRAIN_SITE;QD=14.63;ReadPosRankSum=-0.72;SOR=0.368;VQSLOD=5.79;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:2,4:6:67:116,0,67 -chr6 46803018 rs2297020 A T 292.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.746;ClippingRankSum=0.04;DB;DP=32;FS=3.467;MLEAC=1;MLEAF=0.5;MQ=58.35;MQ0=0;MQRankSum=0.913;POSITIVE_TRAIN_SITE;QD=9.15;ReadPosRankSum=-0.357;SOR=1.659;VQSLOD=2.47;culprit=QD;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:21,11:32:99:321,0,590 -chr6 46803102 rs2297019 A G 273.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.297;ClippingRankSum=-1.681;DB;DP=23;FS=1.74;MLEAC=1;MLEAF=0.5;MQ=58.99;MQ0=0;MQRankSum=-1.484;POSITIVE_TRAIN_SITE;QD=11.9;ReadPosRankSum=-0.495;SOR=0.925;VQSLOD=2.16;culprit=MQRankSum;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:12,10:22:99:302,0,349 -chr6 46803345 rs12196017 G A 98.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.754;ClippingRankSum=0.55;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=52.07;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=14.11;ReadPosRankSum=1.754;SOR=0.941;VQSLOD=6.35;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:3,4:7:96:127,0,96 -chr6 46806766 rs115391170 G A 1395.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-1.528;ClippingRankSum=0.481;DB;DP=95;FS=14.804;MLEAC=1;MLEAF=0.5;MQ=56.8;MQ0=0;MQRankSum=2.724;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=14.69;ReadPosRankSum=1.677;SOR=0.144;VQSLOD=-0.1508;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:44,48:92:99:1424,0,1271 -chr6 46806802 rs143826629 G A 1031.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.214;ClippingRankSum=0.523;DB;DP=71;FS=2.497;MLEAC=1;MLEAF=0.5;MQ=56.16;MQ0=0;MQRankSum=0.719;QD=14.53;ReadPosRankSum=-0.144;SOR=0.401;VQSLOD=1.61;culprit=DP;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:36,35:71:99:1060,0,1434 -chr6 46806809 rs1804211 C T 1130.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.852;ClippingRankSum=0.535;DB;DP=71;FS=1.182;MLEAC=1;MLEAF=0.5;MQ=55.98;MQ0=0;MQRankSum=-0.121;POSITIVE_TRAIN_SITE;QD=15.93;ReadPosRankSum=1.122;SOR=0.995;VQSLOD=3.2;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:34,37:71:99:1159,0,1325 -chr6 46806939 rs17468190 G T 181.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.38;ClippingRankSum=0.244;DB;DP=14;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=46.24;MQ0=0;MQRankSum=-1.977;POSITIVE_TRAIN_SITE;QD=12.98;ReadPosRankSum=0.689;SOR=1.022;VQSLOD=4.95;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 0/1:5,7:12:99:210,0,155 -chr6 46806948 rs150225810 G GTTTGGGGCAGCT 230.82 PASS AC=2;AF=1.0;AN=2;DB;DP=12;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=45.62;MQ0=0;QD=19.23;SOR=3.912;VQSLOD=4.37;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 1/1:0,6:6:17:268,17,0 -chr6 46807040 rs1059276 C A 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.88;culprit=FS;GENE=MEP1A GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 46817550 rs6929917 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46817982 rs6458525 C T 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.65;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 46821191 . A G 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=ADGRF5 GT:AD:DP:GQ:PL 0/1:1,2:3:28:40,0,28 -chr6 46822349 rs475991 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46823695 rs657340 G A 1861.77 PASS AC=2;AF=1.0;AN=2;DB;DP=53;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=56.56;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.21;SOR=1.893;VQSLOD=6.39;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,52:52:99:1890,156,0 -chr6 46823805 rs58687946 A AG 1627.73 PASS AC=2;AF=1.0;AN=2;DB;DP=50;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=55.74;MQ0=0;QD=32.55;SOR=2.511;VQSLOD=4.68;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,46:46:99:1665,138,0 -chr6 46824279 rs526123 A G 176.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.248;ClippingRankSum=1.203;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=45.96;MQ0=0;MQRankSum=-1.683;POSITIVE_TRAIN_SITE;QD=19.64;ReadPosRankSum=-0.573;SOR=1.402;VQSLOD=5.29;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 0/1:3,6:9:92:205,0,92 -chr6 46824448 rs643409 A G 2848.77 PASS AC=2;AF=1.0;AN=2;DB;DP=83;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=34.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.32;SOR=1.816;VQSLOD=7.31;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,83:83:99:2877,250,0 -chr6 46824798 rs521502 C G 420.77 PASS AC=2;AF=1.0;AN=2;DB;DP=11;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.32;SOR=4.977;VQSLOD=6.96;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,11:11:33:449,33,0 -chr6 46825595 rs2281443 G A 37.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.87;SOR=2.303;VQSLOD=8.08;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:65,6,0 -chr6 46825632 rs627910 G C 40.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.37;SOR=2.303;VQSLOD=7.74;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 46826508 rs613870 G A 2427.77 PASS AC=2;AF=1.0;AN=2;DB;DP=67;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.42;SOR=0.917;VQSLOD=7.01;culprit=DP;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,67:67:99:2456,202,0 -chr6 46826715 rs572248 T A 4133.77 PASS AC=2;AF=1.0;AN=2;DB;DP=118;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.35;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.43;SOR=0.881;VQSLOD=6.5;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,114:114:99:4162,343,0 -chr6 46826844 rs571247 T C 5230.77 PASS AC=2;AF=1.0;AN=2;DB;DP=144;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.63;SOR=1.006;VQSLOD=6.93;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,144:144:99:5259,433,0 -chr6 46826910 rs611779 G A 4855.77 PASS AC=2;AF=1.0;AN=2;DB;DP=132;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.04;SOR=1.119;VQSLOD=5.95;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,132:132:99:4884,397,0 -chr6 46826979 rs9381487 A G 1623.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.727;ClippingRankSum=-0.199;DB;DP=106;FS=2.83;MLEAC=1;MLEAF=0.5;MQ=59.82;MQ0=0;MQRankSum=-0.13;POSITIVE_TRAIN_SITE;QD=15.32;ReadPosRankSum=0.117;SOR=1.041;VQSLOD=2.59;culprit=DP;GENE=ADGRF5 GT:AD:DP:GQ:PL 0/1:54,52:106:99:1652,0,1669 -chr6 46827073 rs547499 A G 1003.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.612;ClippingRankSum=-0.887;DB;DP=64;FS=0.955;MLEAC=1;MLEAF=0.5;MQ=58.48;MQ0=0;MQRankSum=-0.699;POSITIVE_TRAIN_SITE;QD=15.68;ReadPosRankSum=-0.094;SOR=0.831;VQSLOD=2.97;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 0/1:31,33:64:99:1032,0,968 -chr6 46827126 rs610856 C T 2450.77 PASS AC=2;AF=1.0;AN=2;DB;DP=64;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.18;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.98;SOR=0.966;VQSLOD=5.61;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,64:64:99:2479,192,0 -chr6 46827239 rs9395218 C T 1247.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.769;ClippingRankSum=-0.087;DB;DP=83;FS=13.228;MLEAC=1;MLEAF=0.5;MQ=51.7;MQ0=0;MQRankSum=0.844;POSITIVE_TRAIN_SITE;QD=15.03;ReadPosRankSum=1.346;SOR=0.158;VQSLOD=1.45;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 0/1:39,44:83:99:1276,0,1186 -chr6 46828670 rs540727 A G 1780.77 PASS AC=2;AF=1.0;AN=2;DB;DP=46;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.96;SOR=4.804;VQSLOD=6.53;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,46:46:99:1809,138,0 -chr6 46830243 rs483813 T C 95.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=1.179;VQSLOD=8.22;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,3:3:9:123,9,0 -chr6 46832536 rs531049 T C 161.9 PASS AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.96;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.38;SOR=3.611;VQSLOD=6.6;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:190,15,0 -chr6 46832553 rs530990 A G 80.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.76;SOR=2.833;VQSLOD=8.23;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,3:3:9:108,9,0 -chr6 46832642 rs615677 A C 985.77 PASS AC=2;AF=1.0;AN=2;DB;DP=26;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.43;SOR=6.593;VQSLOD=7.43;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,26:26:78:1014,78,0 -chr6 46832741 rs529201 T C 4511.77 PASS AC=2;AF=1.0;AN=2;DB;DP=123;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.85;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.57;SOR=3.352;VQSLOD=5.31;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,123:123:99:4540,368,0 -chr6 46832813 rs614826 G A 3006.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-7.723;ClippingRankSum=-0.748;DB;DP=234;FS=8.321;MLEAC=1;MLEAF=0.5;MQ=59.84;MQ0=0;MQRankSum=1.246;POSITIVE_TRAIN_SITE;QD=12.85;ReadPosRankSum=1.65;SOR=1.157;VQSLOD=1.43;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 0/1:127,107:234:99:3035,0,4266 -chr6 46834473 rs586986 T G 189.9 PASS AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.86;SOR=3.611;VQSLOD=5.55;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:218,15,0 -chr6 46834685 rs586024 G A 4443.77 PASS AC=2;AF=1.0;AN=2;DB;DP=121;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.5;SOR=1.857;VQSLOD=6.18;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,121:121:99:4472,364,0 -chr6 46834906 rs5875987 TG T 2501.73 PASS AC=2;AF=1.0;AN=2;DB;DP=69;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.62;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.68;SOR=3.007;VQSLOD=5.93;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,68:68:99:2539,205,0 -chr6 46836406 rs665551 G C 117.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.26;SOR=3.258;VQSLOD=5.89;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,4:4:12:145,12,0 -chr6 46836995 rs515866 T C 146.9 PASS AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.38;SOR=3.611;VQSLOD=6.79;culprit=DP;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:175,15,0 -chr6 46839435 rs58989382 T C 406.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.854;ClippingRankSum=-0.174;DB;DP=24;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.927;POSITIVE_TRAIN_SITE;QD=16.95;ReadPosRankSum=2.202;SOR=0.859;VQSLOD=4.91;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 0/1:11,13:24:99:435,0,357 -chr6 46841306 rs220675 T C 195.8 PASS AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.97;SOR=0.941;VQSLOD=5.21;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,7:7:21:224,21,0 -chr6 46846277 rs220668 G A 565.77 PASS AC=2;AF=1.0;AN=2;DB;DP=15;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.42;SOR=5.549;VQSLOD=6.31;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,15:15:45:594,45,0 -chr6 46847501 rs2273265 T G 803.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=5.965;ClippingRankSum=0.7;DB;DP=55;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.735;POSITIVE_TRAIN_SITE;QD=14.61;ReadPosRankSum=1.889;SOR=1.223;VQSLOD=5.17;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 0/1:31,23:54:99:832,0,1017 -chr6 46849057 rs11760108 G T 191.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.98;ClippingRankSum=0.068;DB;DP=15;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.75;MQ0=0;MQRankSum=0.299;POSITIVE_TRAIN_SITE;QD=12.78;ReadPosRankSum=0.201;SOR=0.693;VQSLOD=6.72;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 0/1:7,7:14:99:220,0,248 -chr6 46852193 rs220663 C T 254.8 PASS AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.99;SOR=4.174;VQSLOD=7.14;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,7:7:21:283,21,0 -chr6 46855734 . C CAGGGAAGAGGACCCAGTAGTTTATCTGCCCA 53.7 PASS AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=5.93;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 46856100 rs678312 G A 5756.77 PASS AC=2;AF=1.0;AN=2;DB;DP=152;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.73;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.1;SOR=1.091;VQSLOD=6.42;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,152:152:99:5785,457,0 -chr6 46858081 rs9472896 T C 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=2.303;VQSLOD=7.76;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 46867717 rs220702 C T 2958.77 PASS AC=2;AF=1.0;AN=2;DB;DP=78;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.4;SOR=3.316;VQSLOD=6.24;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,78:78:99:2987,235,0 -chr6 46867898 rs3215601 TA T 1316.73 PASS AC=2;AF=1.0;AN=2;DB;DP=41;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.26;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.12;SOR=5.892;VQSLOD=4.96;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,38:38:99:1354,114,0 -chr6 46869895 rs220698 T G 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.36;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 46874325 rs114267112 T G 1871.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=5.381;ClippingRankSum=1.525;DB;DP=109;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.943;POSITIVE_TRAIN_SITE;QD=17.17;ReadPosRankSum=2.083;SOR=0.752;VQSLOD=2.72;culprit=MQRankSum;GENE=ADGRF5 GT:AD:DP:GQ:PL 0/1:53,56:109:99:1900,0,1690 -chr6 46895158 rs6458530 C T 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.44;culprit=FS;GENE=ADGRF5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 46928378 rs2396803 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46929606 rs1889578 T C 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.59;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 46931019 rs4714972 T G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46932290 rs9472940 T C 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:32:40,0,32 -chr6 46935422 rs9296519 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46980115 rs1226479 G A 103.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.036;ClippingRankSum=0.365;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.133;POSITIVE_TRAIN_SITE;QD=10.38;ReadPosRankSum=0.741;SOR=0.412;VQSLOD=6.3;culprit=FS;GENE=ADGRF1 GT:AD:DP:GQ:PL 0/1:6,4:10:99:132,0,220 -chr6 46986916 rs1226496 G A 100.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.01;SOR=1.609;VQSLOD=8.14;culprit=FS;GENE=ADGRF1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:128,12,0 -chr6 47015046 rs1352665 G T 49.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=9.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 47029819 rs945217 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47037438 rs1226539 G A 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.26;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 47079304 rs10948329 T G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47106677 . T C 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47116726 rs2003031 C T 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=26.37;SOR=2.303;VQSLOD=6.47;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 47163022 rs76480727 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47176242 rs11368956 C CA 44.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=0.693;VQSLOD=8.41;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 47200360 . AAC A 225.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.751;ClippingRankSum=0.751;DP=18;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.23;MQ0=0;MQRankSum=-0.751;QD=12.54;ReadPosRankSum=-0.751;SOR=3.056;VQSLOD=4.97;culprit=FS;GENE=TNFRSF21 GT:AD:DP:GQ:PL 0/1:1,11:12:4:212,0,4 -chr6 47200703 rs202137000 A C 155.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-6.08;ClippingRankSum=0.291;DB;DP=89;FS=88.069;MLEAC=1;MLEAF=0.5;MQ=56.54;MQ0=0;MQRankSum=-0.508;QD=1.75;ReadPosRankSum=-1.601;SOR=6.868;VQSLOD=-14.2;culprit=FS;GENE=TNFRSF21 GT:AD:DP:GQ:PL 0/1:59,30:89:99:184,0,1744 -chr6 47228836 rs4715001 C A 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=8.8;culprit=FS;GENE=TNFRSF21 GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 47228912 rs10807350 G A 61.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.68;culprit=FS;GENE=TNFRSF21 GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 -chr6 47369341 rs4301296 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47373447 rs1931826 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47425273 rs1889494 T C 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.52;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 47450481 rs9395261 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CD2AP GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47462615 rs2184398 T C 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.42;culprit=FS;GENE=CD2AP GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 47464881 rs62410680 G A 107.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;QD=23.04;SOR=2.833;VQSLOD=7.19;culprit=FS;GENE=CD2AP GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 47464883 rs202187543 G GT 98.25 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;QD=32.75;SOR=2.833;VQSLOD=6.88;culprit=FS;GENE=CD2AP GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 47467043 rs34508069 A ATG 34.71 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.44;MQ0=0;POSITIVE_TRAIN_SITE;QD=11.57;SOR=0.693;VQSLOD=7.53;culprit=FS;GENE=CD2AP GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 -chr6 47470146 rs1564926 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CD2AP GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47489866 rs62410686 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CD2AP GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47494842 rs35617629 T TC 24.72 LowQual AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.44;MQ0=0;QD=8.24;SOR=0.693;GENE=CD2AP GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 -chr6 47512229 rs6915993 C T 472.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.902;ClippingRankSum=-1.52;DB;DP=28;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.645;POSITIVE_TRAIN_SITE;QD=16.88;ReadPosRankSum=-0.369;SOR=0.836;VQSLOD=5.04;culprit=FS;GENE=CD2AP GT:AD:DP:GQ:PL 0/1:13,15:28:99:501,0,447 -chr6 47512590 rs6916578 C T 344.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.172;ClippingRankSum=-0.793;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.34;POSITIVE_TRAIN_SITE;QD=21.55;ReadPosRankSum=-0.566;SOR=1.609;VQSLOD=6.22;culprit=FS;GENE=CD2AP GT:AD:DP:GQ:PL 0/1:5,11:16:99:373,0,169 -chr6 47522357 rs9473132 G A 2114.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.279;ClippingRankSum=0.098;DB;DP=140;FS=1.431;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.117;POSITIVE_TRAIN_SITE;QD=15.11;ReadPosRankSum=-0.616;SOR=0.874;VQSLOD=2.05;culprit=DP;GENE=CD2AP GT:AD:DP:GQ:PL 0/1:66,74:140:99:2143,0,2115 -chr6 47530422 rs9395277 A C 559.77 PASS AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.99;SOR=5.549;VQSLOD=6.68;culprit=QD;GENE=CD2AP GT:AD:DP:GQ:PL 1/1:0,15:15:45:588,45,0 -chr6 47532683 rs9395278 T A 63.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=9.0;culprit=FS;GENE=CD2AP GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 47545058 rs978448 C T 76.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.406;ClippingRankSum=0.406;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.988;POSITIVE_TRAIN_SITE;QD=12.79;ReadPosRankSum=0.406;SOR=2.093;VQSLOD=6.6;culprit=FS;GENE=CD2AP GT:AD:DP:GQ:PL 0/1:3,3:6:99:105,0,105 -chr6 47548672 rs1014001 C A 2124.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.361;ClippingRankSum=1.15;DB;DP=186;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.8;MQ0=0;MQRankSum=1.434;POSITIVE_TRAIN_SITE;QD=11.42;ReadPosRankSum=-1.001;SOR=0.701;VQSLOD=1.41;culprit=FS;GENE=CD2AP GT:AD:DP:GQ:PL 0/1:112,73:185:99:2153,0,3635 -chr6 47549586 rs6926592 A T 31.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=45.47;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=3.53;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=5.09;culprit=QD;GENE=CD2AP GT:AD:DP:GQ:PL 0/1:2,2:4:60:60,0,65 -chr6 47549883 rs2275446 T C 1040.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=5.815;ClippingRankSum=-1.023;DB;DP=59;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.902;POSITIVE_TRAIN_SITE;QD=17.64;ReadPosRankSum=1.327;SOR=1.609;VQSLOD=5.52;culprit=FS;GENE=CD2AP GT:AD:DP:GQ:PL 0/1:30,29:59:99:1069,0,967 -chr6 47563692 rs2039503 C T 15612.77 PASS AC=2;AF=1.0;AN=2;DB;DP=434;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.93;MQ0=0;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=32.86;SOR=1.288;VQSLOD=0.729;culprit=DP;GENE=CD2AP GT:AD:DP:GQ:PL 1/1:0,433:433:99:15641,1302,0 -chr6 47577064 rs9395287 G A 1930.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.08;ClippingRankSum=-0.414;DB;DP=155;FS=5.202;MLEAC=1;MLEAF=0.5;MQ=59.55;MQ0=0;MQRankSum=1.011;POSITIVE_TRAIN_SITE;QD=12.46;ReadPosRankSum=1.551;SOR=0.345;VQSLOD=2.02;culprit=DP;GENE=CD2AP GT:AD:DP:GQ:PL 0/1:89,66:155:99:1959,0,2911 -chr6 47591856 rs10948368 T C 837.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.469;ClippingRankSum=1.334;DB;DP=42;FS=3.025;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.826;POSITIVE_TRAIN_SITE;QD=19.95;ReadPosRankSum=1.309;SOR=0.151;VQSLOD=2.32;culprit=QD;GENE=CD2AP GT:AD:DP:GQ:PL 0/1:18,24:42:99:866,0,595 -chr6 47592328 rs11309569 GT G 75.25 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.08;SOR=1.179;VQSLOD=8.27;culprit=FS;GENE=CD2AP GT:AD:DP:GQ:PL 1/1:0,3:3:9:112,9,0 -chr6 47611404 rs13196954 C G 36.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.937;ClippingRankSum=0.0;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=5.25;ReadPosRankSum=0.937;SOR=0.446;VQSLOD=4.88;culprit=QD GT:AD:DP:GQ:PL 0/1:4,3:7:65:65,0,111 -chr6 47611442 rs7766527 T C 84.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.0;ClippingRankSum=-0.421;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-2.017;POSITIVE_TRAIN_SITE;QD=10.6;ReadPosRankSum=0.421;SOR=1.609;VQSLOD=4.55;culprit=FS GT:AD:DP:GQ:PL 0/1:4,4:8:99:113,0,102 -chr6 47624115 rs1485782 C T 140.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.922;ClippingRankSum=0.198;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.03;MQ0=0;MQRankSum=-0.922;POSITIVE_TRAIN_SITE;QD=20.11;ReadPosRankSum=1.495;SOR=1.609;VQSLOD=5.61;culprit=FS;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:2,5:7:57:169,0,57 -chr6 47624129 rs1485783 G A 221.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.733;ClippingRankSum=-0.898;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=52.65;MQ0=0;MQRankSum=-0.48;POSITIVE_TRAIN_SITE;QD=22.18;ReadPosRankSum=0.48;SOR=2.303;VQSLOD=5.41;culprit=FS;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:2,8:10:57:250,0,57 -chr6 47624239 rs1485784 A G 779.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.26;ClippingRankSum=-1.087;DB;DP=42;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.33;MQ0=0;MQRankSum=-0.455;POSITIVE_TRAIN_SITE;QD=18.57;ReadPosRankSum=-1.744;SOR=0.286;VQSLOD=5.1;culprit=FS;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:19,23:42:99:808,0,614 -chr6 47624299 rs9369730 A G 990.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.981;ClippingRankSum=0.405;DB;DP=68;FS=2.459;MLEAC=1;MLEAF=0.5;MQ=56.52;MQ0=0;MQRankSum=-0.459;POSITIVE_TRAIN_SITE;QD=14.57;ReadPosRankSum=2.549;SOR=0.389;VQSLOD=2.9;culprit=ReadPosRankSum;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:29,35:64:99:1019,0,894 -chr6 47624633 rs1021231 G A 201.84 PASS AC=2;AF=1.0;AN=2;DB;DP=6;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=56.04;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.64;SOR=3.912;VQSLOD=7.41;culprit=FS;GENE=ADGRF2 GT:AD:DP:GQ:PL 1/1:0,6:6:18:230,18,0 -chr6 47626149 rs6934553 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=ADGRF2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47626490 rs10456129 G C 47.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=15.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=6.4;culprit=FS;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:1,2:3:30:76,0,30 -chr6 47626685 rs6935668 C T 505.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.678;ClippingRankSum=-0.091;DB;DP=50;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.677;POSITIVE_TRAIN_SITE;QD=10.12;ReadPosRankSum=-0.677;SOR=0.67;VQSLOD=4.29;culprit=FS;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:32,18:50:99:534,0,1085 -chr6 47626833 rs12201065 C A 1126.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.697;ClippingRankSum=-0.211;DB;DP=79;FS=1.842;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.624;POSITIVE_TRAIN_SITE;QD=14.26;ReadPosRankSum=2.098;SOR=0.509;VQSLOD=3.19;culprit=ReadPosRankSum;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:42,37:79:99:1155,0,1430 -chr6 47631622 rs2396829 G T 13.72 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=6.86;SOR=1.609;GENE=ADGRF2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 -chr6 47641307 rs1411049 G C 1221.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-6.168;ClippingRankSum=0.23;DB;DP=74;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.479;POSITIVE_TRAIN_SITE;QD=16.51;ReadPosRankSum=-0.34;SOR=1.061;VQSLOD=4.74;culprit=FS;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:31,43:74:99:1250,0,1019 -chr6 47645772 rs9369734 G T 131.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.387;ClippingRankSum=-0.717;DB;DP=11;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.87;MQ0=0;MQRankSum=1.186;POSITIVE_TRAIN_SITE;QD=11.98;ReadPosRankSum=1.031;SOR=0.551;VQSLOD=4.95;culprit=FS;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:6,5:11:99:160,0,198 -chr6 47646468 rs6929227 T C 36.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=12.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=5.87;culprit=FS;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:1,2:3:33:65,0,33 -chr6 47646842 rs6907125 A G 1474.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.856;ClippingRankSum=0.375;DB;DP=112;FS=1.527;MLEAC=1;MLEAF=0.5;MQ=59.83;MQ0=0;MQRankSum=-0.67;POSITIVE_TRAIN_SITE;QD=13.17;ReadPosRankSum=-0.351;SOR=0.896;VQSLOD=2.99;culprit=DP;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:57,54:111:99:1503,0,1770 -chr6 47647004 rs6911739 C T 236.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.835;ClippingRankSum=-0.289;DB;DP=14;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.536;POSITIVE_TRAIN_SITE;QD=16.91;ReadPosRankSum=0.289;SOR=0.495;VQSLOD=6.19;culprit=FS;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:4,8:12:99:265,0,101 -chr6 47647593 rs58870329 GA G 32.74 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=10.91;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=6.02;culprit=FS;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:1,2:3:30:70,0,30 -chr6 47649222 rs8180544 T G 3766.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.617;ClippingRankSum=-0.635;DB;DP=262;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.75;MQ0=0;MQRankSum=-0.348;POSITIVE_TRAIN_SITE;QD=14.38;ReadPosRankSum=1.474;SOR=0.706;VQSLOD=1.98;culprit=FS;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:130,131:261:99:3795,0,4054 -chr6 47649265 rs17541107 T A 4039.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.52;ClippingRankSum=0.331;DB;DP=283;FS=5.506;MLEAC=1;MLEAF=0.5;MQ=59.84;MQ0=0;MQRankSum=-0.377;POSITIVE_TRAIN_SITE;QD=14.27;ReadPosRankSum=1.57;SOR=0.994;VQSLOD=1.83;culprit=DP;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:148,135:283:99:4068,0,4356 -chr6 47649573 rs10807371 C T 3884.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.363;ClippingRankSum=0.166;DB;DP=210;FS=0.513;MLEAC=1;MLEAF=0.5;MQ=59.82;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=18.5;ReadPosRankSum=2.787;SOR=0.633;VQSLOD=1.64;culprit=FS;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:110,99:209:99:3913,0,7372 -chr6 47649574 rs10807372 A G 3884.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=5.254;ClippingRankSum=0.771;DB;DP=211;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.82;MQ0=0;MQRankSum=1.085;POSITIVE_TRAIN_SITE;QD=18.41;ReadPosRankSum=2.423;SOR=0.713;VQSLOD=1.59;culprit=FS;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:108,102:210:99:3913,0,7372 -chr6 47649694 rs9381594 A G 2384.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.217;ClippingRankSum=0.797;DB;DP=160;FS=5.307;MLEAC=1;MLEAF=0.5;MQ=59.71;MQ0=0;MQRankSum=0.869;POSITIVE_TRAIN_SITE;QD=14.9;ReadPosRankSum=0.046;SOR=1.179;VQSLOD=2.22;culprit=DP;GENE=ADGRF2 GT:AD:DP:GQ:PL 0/1:82,78:160:99:2413,0,2636 -chr6 47653485 rs9369736 A G 580.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.376;ClippingRankSum=-0.637;DB;DP=39;FS=6.87;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.099;POSITIVE_TRAIN_SITE;QD=14.89;ReadPosRankSum=1.119;SOR=2.2;VQSLOD=2.66;culprit=FS;GENE=ADGRF4,ADGRF2 GT:AD:DP:GQ:PL 0/1:22,17:39:99:609,0,665 -chr6 47653536 rs9381596 A G 676.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.398;ClippingRankSum=-1.699;DB;DP=50;FS=5.655;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.621;POSITIVE_TRAIN_SITE;QD=13.54;ReadPosRankSum=1.097;SOR=1.197;VQSLOD=1.88;culprit=FS;GENE=ADGRF4,ADGRF2 GT:AD:DP:GQ:PL 0/1:26,24:50:99:705,0,787 -chr6 47654591 rs10948376 G T 642.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.972;ClippingRankSum=-0.822;DB;DP=39;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.782;POSITIVE_TRAIN_SITE;QD=16.48;ReadPosRankSum=-0.752;SOR=1.085;VQSLOD=3.73;culprit=MQRankSum;GENE=ADGRF4,ADGRF2 GT:AD:DP:GQ:PL 0/1:14,20:34:99:671,0,497 -chr6 47654662 rs10485315 A G 2893.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=7.315;ClippingRankSum=0.398;DB;DP=167;FS=1.004;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.357;POSITIVE_TRAIN_SITE;QD=17.33;ReadPosRankSum=2.188;SOR=0.957;VQSLOD=2.61;culprit=FS;GENE=ADGRF4,ADGRF2 GT:AD:DP:GQ:PL 0/1:84,83:167:99:2922,0,2748 -chr6 47654742 rs9296573 A T 4359.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.866;ClippingRankSum=0.983;DB;DP=296;FS=5.331;MLEAC=1;MLEAF=0.5;MQ=59.8;MQ0=0;MQRankSum=0.493;POSITIVE_TRAIN_SITE;QD=14.73;ReadPosRankSum=-1.261;SOR=0.468;VQSLOD=1.31;culprit=DP;GENE=ADGRF4,ADGRF2 GT:AD:DP:GQ:PL 0/1:143,153:296:99:4388,0,4431 -chr6 47654817 rs1556133 C A 3193.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-6.266;ClippingRankSum=-0.767;DB;DP=141;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.607;POSITIVE_TRAIN_SITE;QD=22.65;ReadPosRankSum=0.439;SOR=0.716;VQSLOD=2.57;culprit=FS;GENE=ADGRF4,ADGRF2 GT:AD:DP:GQ:PL 0/1:57,84:141:99:3222,0,2060 -chr6 47654831 rs1556132 A G 3144.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=5.124;ClippingRankSum=-0.737;DB;DP=121;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.55;POSITIVE_TRAIN_SITE;QD=25.99;ReadPosRankSum=0.045;SOR=0.73;VQSLOD=2.91;culprit=FS;GENE=ADGRF4,ADGRF2 GT:AD:DP:GQ:PL 0/1:47,74:121:99:3173,0,1780 -chr6 47654864 rs1556131 T G 1356.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.916;ClippingRankSum=1.761;DB;DP=69;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.023;POSITIVE_TRAIN_SITE;QD=19.66;ReadPosRankSum=-0.03;SOR=0.98;VQSLOD=4.41;culprit=FS;GENE=ADGRF4,ADGRF2 GT:AD:DP:GQ:PL 0/1:30,39:69:99:1385,0,976 -chr6 47661115 rs6901702 T C 90.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.09;SOR=2.833;VQSLOD=7.91;culprit=FS;GENE=ADGRF4,ADGRF2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:118,9,0 -chr6 47661248 rs36010404 AG A 335.73 PASS AC=2;AF=1.0;AN=2;DB;DP=12;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.98;SOR=4.977;VQSLOD=6.17;culprit=FS;GENE=ADGRF4,ADGRF2 GT:AD:DP:GQ:PL 1/1:0,11:11:33:373,33,0 -chr6 47661260 rs200900695 AC A 126.76 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.589;ClippingRankSum=-0.354;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=50.65;MQ0=0;MQRankSum=-1.768;POSITIVE_TRAIN_SITE;QD=7.92;ReadPosRankSum=1.061;SOR=2.494;VQSLOD=4.52;culprit=FS;GENE=ADGRF4,ADGRF2 GT:AD:DP:GQ:PL 0/1:2,9:11:22:164,0,22 -chr6 47661387 rs9395311 A G 2320.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.015;ClippingRankSum=-0.577;DB;DP=139;FS=8.901;MLEAC=1;MLEAF=0.5;MQ=59.67;MQ0=0;MQRankSum=-0.615;POSITIVE_TRAIN_SITE;QD=16.7;ReadPosRankSum=2.635;SOR=0.237;VQSLOD=1.11;culprit=FS;GENE=ADGRF4,ADGRF2 GT:AD:DP:GQ:PL 0/1:64,75:139:99:2349,0,1921 -chr6 47675922 rs16876334 C T 1527.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.988;ClippingRankSum=-0.373;DB;DP=82;FS=4.427;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.181;POSITIVE_TRAIN_SITE;QD=18.63;ReadPosRankSum=0.624;SOR=1.413;VQSLOD=1.23;culprit=MQRankSum;GENE=ADGRF4 GT:AD:DP:GQ:PL 0/1:37,45:82:99:1556,0,1063 -chr6 47676150 rs9369737 C T 269.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.291;ClippingRankSum=1.732;DB;DP=23;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.283;POSITIVE_TRAIN_SITE;QD=11.73;ReadPosRankSum=-0.346;SOR=0.368;VQSLOD=5.18;culprit=FS;GENE=ADGRF4 GT:AD:DP:GQ:PL 0/1:14,9:23:99:298,0,504 -chr6 47678455 rs11356177 CT C 1687.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.012;ClippingRankSum=-0.222;DB;DP=162;FS=0.656;MLEAC=1;MLEAF=0.5;MQ=60.33;MQ0=0;MQRankSum=1.477;POSITIVE_TRAIN_SITE;QD=10.42;ReadPosRankSum=0.632;SOR=0.809;VQSLOD=1.77;culprit=FS;GENE=ADGRF4 GT:AD:DP:GQ:PL 0/1:80,76:156:99:1725,0,2007 -chr6 47678678 rs944056 C G 3493.77 PASS AC=2;AF=1.0;AN=2;DB;DP=91;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.59;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.34;SOR=2.758;VQSLOD=7.4;culprit=FS;GENE=ADGRF4 GT:AD:DP:GQ:PL 1/1:0,90:90:99:3522,271,0 -chr6 47678718 rs1318391 C G 857.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.618;ClippingRankSum=0.693;DB;DP=61;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.08;POSITIVE_TRAIN_SITE;QD=14.06;ReadPosRankSum=0.97;SOR=0.439;VQSLOD=5.75;culprit=FS;GENE=ADGRF4 GT:AD:DP:GQ:PL 0/1:35,26:61:99:886,0,1329 -chr6 47678848 rs199503700 CAA C 43.74 PASS AC=1;AF=0.5;AN=2;DB;DP=2;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.87;SOR=2.303;VQSLOD=8.58;culprit=FS;GENE=ADGRF4 GT:AD:DP:GQ:PL 0/1:0,2:2:25:81,0,25 -chr6 47678861 rs9381602 A G 52.78 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.93;culprit=FS;GENE=ADGRF4 GT:AD:DP:GQ:PL 0/1:1,2:3:25:81,0,25 -chr6 47680450 rs871654 A C 516.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.618;ClippingRankSum=-0.634;DB;DP=21;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.41;POSITIVE_TRAIN_SITE;QD=24.61;ReadPosRankSum=0.634;SOR=1.508;VQSLOD=5.59;culprit=FS;GENE=ADGRF4 GT:AD:DP:GQ:PL 0/1:7,14:21:99:545,0,211 -chr6 47681494 rs6916562 T C 3414.77 PASS AC=2;AF=1.0;AN=2;DB;DP=86;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.92;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.9;SOR=5.235;VQSLOD=6.11;culprit=FS;GENE=ADGRF4 GT:AD:DP:GQ:PL 1/1:0,86:86:99:3443,259,0 -chr6 47682604 rs9369738 A C 6287.77 PASS AC=2;AF=1.0;AN=2;DB;DP=181;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.74;SOR=1.468;VQSLOD=6.07;culprit=QD;GENE=ADGRF4,RN7SKP116 GT:AD:DP:GQ:PL 1/1:0,179:179:99:6316,538,0 -chr6 47682949 rs16876369 C T 1708.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.057;ClippingRankSum=-0.481;DB;DP=110;FS=7.189;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.072;POSITIVE_TRAIN_SITE;QD=15.53;ReadPosRankSum=0.146;SOR=1.458;VQSLOD=1.58;culprit=FS;GENE=ADGRF4,RN7SKP116 GT:AD:DP:GQ:PL 0/1:54,56:110:99:1737,0,1465 -chr6 47683057 rs41452951 A G 376.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.298;ClippingRankSum=-0.209;DB;DP=28;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.17;MQ0=0;MQRankSum=0.07;POSITIVE_TRAIN_SITE;QD=13.46;ReadPosRankSum=0.07;SOR=0.46;VQSLOD=5.39;culprit=FS;GENE=ADGRF4,RN7SKP116 GT:AD:DP:GQ:PL 0/1:16,12:28:99:405,0,546 -chr6 47684591 rs1360157 G A 2096.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.035;ClippingRankSum=0.291;DB;DP=146;FS=1.305;MLEAC=1;MLEAF=0.5;MQ=59.71;MQ0=0;MQRankSum=0.615;POSITIVE_TRAIN_SITE;QD=14.36;ReadPosRankSum=0.971;SOR=0.572;VQSLOD=3.15;culprit=DP;GENE=ADGRF4 GT:AD:DP:GQ:PL 0/1:74,71:145:99:2125,0,2159 -chr6 47686101 rs6914013 T C 9061.77 PASS AC=2;AF=1.0;AN=2;DB;DP=255;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.93;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.19;SOR=1.281;VQSLOD=5.11;culprit=FS;GENE=ADGRF4 GT:AD:DP:GQ:PL 1/1:0,254:254:99:9090,763,0 -chr6 47686235 rs11754756 C A 1895.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.892;ClippingRankSum=1.54;DB;DP=110;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.66;MQ0=0;MQRankSum=0.867;POSITIVE_TRAIN_SITE;QD=17.23;ReadPosRankSum=-0.771;SOR=0.905;VQSLOD=3.88;culprit=FS;GENE=ADGRF4 GT:AD:DP:GQ:PL 0/1:50,60:110:99:1924,0,1695 -chr6 47686397 rs11476874 AT A 63.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.358;ClippingRankSum=-0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=62.13;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=12.75;ReadPosRankSum=0.358;SOR=1.022;VQSLOD=6.6;culprit=FS;GENE=ADGRF4 GT:AD:DP:GQ:PL 0/1:2,3:5:66:101,0,66 -chr6 47690579 rs1329522 T C 91.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.76;SOR=0.693;VQSLOD=6.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:119,12,0 -chr6 47690601 rs35597357 T C 29.77 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.026;QD=7.44;ReadPosRankSum=0.0;SOR=0.693 GT:AD:DP:GQ:PL 0/1:2,2:4:37:58,0,37 -chr6 47690613 rs1329523 G A 81.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.09;SOR=1.179;VQSLOD=8.5;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:109,9,0 -chr6 47696780 rs2282337 C T 36.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.38;ClippingRankSum=-0.72;DB;DP=6;FS=3.31;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=6.13;ReadPosRankSum=-0.72;SOR=2.303;VQSLOD=2.06;culprit=QD GT:AD:DP:GQ:PL 0/1:4,2:6:65:65,0,81 -chr6 47698280 rs1329540 G A 94.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=1.179;VQSLOD=8.91;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:122,9,0 -chr6 47698303 rs1329539 C T 94.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=1.179;VQSLOD=7.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:122,9,0 -chr6 47703969 rs949680 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47707247 rs72864549 C T 37.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.87;SOR=2.303;VQSLOD=6.9;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:65,6,0 -chr6 47708230 rs12199415 A G 96.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.09;SOR=1.179;VQSLOD=7.86;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:124,9,0 -chr6 47708267 rs9473166 C T 93.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.09;SOR=1.179;VQSLOD=6.97;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:121,9,0 -chr6 47712313 rs9349429 T G 41.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.87;SOR=2.303;VQSLOD=8.76;culprit=QD GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 -chr6 47714073 rs9367302 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47720533 rs61744507 G A 144.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.876;ClippingRankSum=-1.652;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.361;POSITIVE_TRAIN_SITE;QD=16.09;ReadPosRankSum=1.881;SOR=0.892;VQSLOD=5.73;culprit=FS GT:AD:DP:GQ:PL 0/1:4,5:9:99:173,0,134 -chr6 47720824 rs2039141 A G 2982.77 PASS AC=2;AF=1.0;AN=2;DB;DP=82;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.72;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.6;SOR=1.697;VQSLOD=5.16;culprit=FS GT:AD:DP:GQ:PL 1/1:0,82:82:99:3011,247,0 -chr6 47740398 rs1329529 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47746444 rs10485318 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47749539 rs9395320 A G 59.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=9.35;culprit=FS;GENE=OPN5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 47749728 rs7741473 T G 1371.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.498;ClippingRankSum=1.007;DB;DP=64;FS=3.91;MLEAC=1;MLEAF=0.5;MQ=58.91;MQ0=0;MQRankSum=0.168;POSITIVE_TRAIN_SITE;QD=21.43;ReadPosRankSum=-0.21;SOR=0.253;VQSLOD=2.29;culprit=QD;GENE=OPN5 GT:AD:DP:GQ:PL 0/1:23,41:64:99:1400,0,654 -chr6 47754498 rs1329543 A G 352.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.647;ClippingRankSum=-0.208;DB;DP=26;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.052;POSITIVE_TRAIN_SITE;QD=13.57;ReadPosRankSum=0.052;SOR=0.446;VQSLOD=5.83;culprit=FS;GENE=OPN5 GT:AD:DP:GQ:PL 0/1:15,11:26:99:381,0,529 -chr6 47754538 rs6900985 T C 166.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.859;ClippingRankSum=-1.156;DB;DP=17;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.653;POSITIVE_TRAIN_SITE;QD=9.81;ReadPosRankSum=0.653;SOR=0.293;VQSLOD=5.2;culprit=FS;GENE=OPN5 GT:AD:DP:GQ:PL 0/1:11,6:17:99:195,0,378 -chr6 47763514 rs139235050 TCACACA T 98.25 PASS AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=44.1;MQ0=0;QD=19.65;SOR=2.833;VQSLOD=6.81;culprit=FS;GENE=OPN5 GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 47808012 rs474725 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47822105 rs532671 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47826378 rs476873 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47841953 rs4715047 G T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47845813 rs1887899 G T 171.9 PASS AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.38;SOR=3.611;VQSLOD=7.2;culprit=FS;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,5:5:15:200,15,0 -chr6 47847179 rs3799276 A G 11221.77 PASS AC=2;AF=1.0;AN=2;DB;DP=302;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.72;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.02;SOR=1.221;VQSLOD=2.8;culprit=FS;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,301:301:99:11250,905,0 -chr6 47847401 rs2068006 A G 6414.77 PASS AC=2;AF=1.0;AN=2;DB;DP=184;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.86;SOR=0.832;VQSLOD=4.02;culprit=QD;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,182:182:99:6443,547,0 -chr6 47847683 rs9367307 A T 3379.77 PASS AC=2;AF=1.0;AN=2;DB;DP=142;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.8;SOR=3.095;VQSLOD=3.37;culprit=FS;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,121:121:99:3408,364,0 -chr6 47862643 rs113155505 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47865882 rs4715053 G C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47869426 rs1360080 A G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=9.52;culprit=FS;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 47869448 rs1360081 G A 125.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.26;SOR=1.609;VQSLOD=7.95;culprit=FS;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,4:4:12:153,12,0 -chr6 47871871 rs13194591 C T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.67;culprit=FS;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 47871877 . A G 62.74 PASS AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.51;culprit=FS;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 47927739 . A T 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47941339 rs2753188 G A 61.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=6.28;culprit=FS;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 -chr6 47954722 rs2145363 C A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47977018 rs2753194 C A 684.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.07;ClippingRankSum=1.38;DB;DP=36;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.36;MQ0=0;MQRankSum=0.995;POSITIVE_TRAIN_SITE;QD=19.02;ReadPosRankSum=1.508;SOR=1.061;VQSLOD=4.96;culprit=FS;GENE=PTCHD4 GT:AD:DP:GQ:PL 0/1:15,21:36:99:713,0,543 -chr6 47977136 rs45599036 C T 79.78 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.727;POSITIVE_TRAIN_SITE;QD=19.94;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=5.45;culprit=FS;GENE=PTCHD4 GT:AD:DP:GQ:PL 0/1:1,3:4:26:108,0,26 -chr6 48005879 rs12205869 G A 45.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=0.693;VQSLOD=9.01;culprit=FS;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 -chr6 48009812 . A C 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223;GENE=PTCHD4 GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 -chr6 48015295 rs618543 T G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48015693 rs332554 A G 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=7.12;culprit=FS;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 48026377 rs647942 A G 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=9.17;culprit=FS;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 48032884 rs75735764 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PTCHD4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48036051 rs201541883 A C 779.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-6.322;ClippingRankSum=-0.178;DB;DP=120;FS=165.662;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=-0.683;QD=6.5;ReadPosRankSum=-4.265;SOR=8.379;VQSLOD=-62.04;culprit=FS;GENE=PTCHD4 GT:AD:DP:GQ:PL 0/1:52,65:117:99:808,0,1315 -chr6 48083008 rs6908563 G A 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.84;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 48117685 rs12523977 C G 501.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.424;ClippingRankSum=0.073;DB;DP=38;FS=1.785;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.833;POSITIVE_TRAIN_SITE;QD=13.2;ReadPosRankSum=-2.675;SOR=1.329;VQSLOD=1.85;culprit=ReadPosRankSum;GENE=HNRNPA3P4 GT:AD:DP:GQ:PL 0/1:20,18:38:99:530,0,640 -chr6 48131753 rs1331118 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48172099 . G GGGA 46.7 PASS AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=23.35;SOR=0.693;VQSLOD=5.94;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 48195386 . A G 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48214766 rs2456916 A G 38.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=12.92;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=5.88;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:33:67,0,33 -chr6 48214812 rs2503669 C G 78.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=1.754;ClippingRankSum=0.937;DB;DP=7;FS=15.441;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.55;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=11.25;ReadPosRankSum=1.3;SOR=2.775;VQSLOD=0.03;culprit=FS GT:AD:DP:GQ:PL 0/1:4,3:7:99:107,0,141 -chr6 48214977 rs2503670 A G 44.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.0;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=11.19;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=6.4;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:71:73,0,71 -chr6 48215008 rs2496375 G A 41.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.0;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=10.44;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=6.07;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:70:70,0,71 -chr6 48225108 . A G 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48262773 rs13202212 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48282517 rs11758955 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48282542 rs545090 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48396334 rs9473361 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48445933 rs1121646 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48448275 rs9473387 A T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48449928 . C A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48450548 rs9784854 G A 47.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=2.303;VQSLOD=7.59;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 48456067 rs148792649 CAGTCTTGAAGACAAAATGCTAACATGTAATAAGAAAATATTTGA C 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=7.01;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 48456290 rs7754822 G T 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 48456315 rs9473391 A T 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=9.25;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 48464593 rs9473403 G T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48467616 rs12206390 A G 65.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.76;SOR=1.179;VQSLOD=8.09;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:93,9,0 -chr6 48468120 rs6915049 A T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48592097 . G A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48596846 rs2912621 T G 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 48609036 rs963049 G C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48615474 rs2433657 A T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48750072 rs2495881 T C 75.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.09;SOR=2.833;VQSLOD=7.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:103,9,0 -chr6 48792612 rs2495863 C T 62.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.73;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 48811854 . C A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48825657 rs1938202 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48899692 rs10948458 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48919773 rs16878430 G A 235.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.54;ClippingRankSum=-0.212;DB;DP=16;FS=4.467;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.318;POSITIVE_TRAIN_SITE;QD=14.74;ReadPosRankSum=-1.059;SOR=0.525;VQSLOD=3.12;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:7,9:16:99:264,0,243 -chr6 48920376 rs12204534 C T 96.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.09;SOR=2.833;VQSLOD=7.58;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:124,9,0 -chr6 49011686 rs35984632 A AT 50.25 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=63.51;MQ0=0;QD=16.75;SOR=1.179;VQSLOD=7.07;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:87,9,0 -chr6 49022228 rs6458657 C A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49036510 rs12194577 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49045630 rs9367346 A T 789.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.471;ClippingRankSum=-1.379;DB;DP=53;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.098;POSITIVE_TRAIN_SITE;QD=14.9;ReadPosRankSum=2.233;SOR=0.793;VQSLOD=5.52;culprit=FS GT:AD:DP:GQ:PL 0/1:27,26:53:99:818,0,792 -chr6 49052341 rs6458676 A G 38.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=7.75;ReadPosRankSum=-0.358;SOR=1.179;VQSLOD=5.43;culprit=QD GT:AD:DP:GQ:PL 0/1:2,3:5:34:67,0,34 -chr6 49083404 . A G 43.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.0;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.026;QD=10.94;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=3.54;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:61:72,0,61 -chr6 49169185 rs113197207 C CTTCT 77.25 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.53;SOR=0.693;VQSLOD=8.18;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:9:114,9,0 -chr6 49199384 rs570913 T G 15.65 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=15.65;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0 -chr6 49209747 rs9463466 G T 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.39;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 49212193 rs492254 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49218084 rs7756663 G A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 49218093 rs11453208 A AT 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=6.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 49397107 . A G 12.06 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:26:40,0,26 -chr6 49414272 . A G 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=MUT GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49415351 . TA T 91.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.54;ClippingRankSum=-0.501;DP=115;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.85;MQ0=0;MQRankSum=0.642;POSITIVE_TRAIN_SITE;QD=0.8;ReadPosRankSum=0.146;SOR=0.653;VQSLOD=3.81;culprit=FS;GENE=MUT GT:AD:DP:GQ:PL 0/1:57,17:74:99:129,0,1146 -chr6 49437853 rs11333073 AT A 27.74 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.412;ClippingRankSum=-0.483;DB;DP=50;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.69;MQ0=0;MQRankSum=0.985;QD=0.55;ReadPosRankSum=0.77;SOR=0.976;GENE=CENPQ GT:AD:DP:GQ:PL 0/1:38,8:46:65:65,0,808 -chr6 49456545 rs2501965 G A 816.77 PASS AC=2;AF=1.0;AN=2;DB;DP=22;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=33.39;SOR=6.273;VQSLOD=4.58;culprit=FS;GENE=CENPQ GT:AD:DP:GQ:PL 1/1:0,22:22:66:845,66,0 -chr6 49459978 rs2501968 A G 4668.77 PASS AC=2;AF=1.0;AN=2;DB;DP=126;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.08;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.08;SOR=1.981;VQSLOD=6.45;culprit=FS;GENE=CENPQ GT:AD:DP:GQ:PL 1/1:0,124:124:99:4697,373,0 -chr6 49460152 rs1471539 A G 177.9 PASS AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.65;SOR=3.611;VQSLOD=5.84;culprit=FS;GENE=CENPQ GT:AD:DP:GQ:PL 1/1:0,5:5:15:206,15,0 -chr6 49479750 rs13193063 T C 340.77 PASS AC=2;AF=1.0;AN=2;DB;DP=12;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.4;SOR=1.445;VQSLOD=6.2;culprit=FS;GENE=GLYATL3 GT:AD:DP:GQ:PL 1/1:0,12:12:36:369,36,0 -chr6 49479775 rs1480615 A T 224.8 PASS AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.11;SOR=2.584;VQSLOD=7.65;culprit=FS;GENE=GLYATL3 GT:AD:DP:GQ:PL 1/1:0,7:7:21:253,21,0 -chr6 49480339 rs9463493 A G 64.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=1.179;VQSLOD=8.26;culprit=FS;GENE=GLYATL3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:92,9,0 -chr6 49494241 rs9367359 A G 3361.77 PASS AC=2;AF=1.0;AN=2;DB;DP=95;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.6;SOR=0.826;VQSLOD=7.14;culprit=FS;GENE=GLYATL3 GT:AD:DP:GQ:PL 1/1:0,94:94:99:3390,283,0 -chr6 49495862 rs6458696 T G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=GLYATL3 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49497461 rs2396905 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49508103 rs9463500 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49515525 rs4715136 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49518914 rs6919674 C G 44.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.37;SOR=2.303;VQSLOD=8.57;culprit=FS;GENE=C6orf141 GT:AD:DP:GQ:PL 1/1:0,2:2:6:72,6,0 -chr6 49522920 . T A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=C6orf141 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49528183 rs6899583 A G 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=7.73;culprit=FS;GENE=C6orf141 GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 49537956 rs36081197 T A 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.79;culprit=FS;GENE=CYP2AC1P GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 49559793 rs10948514 G T 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=8.84;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 49596219 rs4711931 T C 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.2;culprit=FS;GENE=RHAG GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 49646966 rs7763840 T C 66.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.09;SOR=1.179;VQSLOD=8.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:94,9,0 -chr6 49650193 rs148454607 CCCT C 84.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=-0.727;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=62.13;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=16.95;ReadPosRankSum=0.727;SOR=0.916;VQSLOD=6.11;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:37:122,0,37 -chr6 49660418 rs12624 A C 1647.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.101;ClippingRankSum=-1.338;DB;DP=95;FS=5.883;MLEAC=1;MLEAF=0.5;MQ=59.76;MQ0=0;MQRankSum=-1.323;POSITIVE_TRAIN_SITE;QD=17.34;ReadPosRankSum=0.011;SOR=1.333;VQSLOD=1.55;culprit=FS;GENE=CRISP2 GT:AD:DP:GQ:PL 0/1:42,53:95:99:1676,0,1201 -chr6 49663465 rs2248263 G A 603.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.236;ClippingRankSum=0.133;DB;DP=33;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.43;MQ0=0;MQRankSum=0.399;POSITIVE_TRAIN_SITE;QD=18.3;ReadPosRankSum=0.589;SOR=0.957;VQSLOD=5.69;culprit=FS;GENE=CRISP2 GT:AD:DP:GQ:PL 0/1:14,18:32:99:632,0,410 -chr6 49665120 rs10548881 GGT G 34.71 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=63.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=11.57;SOR=2.303;VQSLOD=8.54;culprit=FS;GENE=CRISP2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 -chr6 49666381 rs515257 G A 145.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.886;ClippingRankSum=-1.798;DB;DP=19;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.395;POSITIVE_TRAIN_SITE;QD=7.67;ReadPosRankSum=1.184;SOR=0.223;VQSLOD=5.06;culprit=QD;GENE=CRISP2 GT:AD:DP:GQ:PL 0/1:13,6:19:99:174,0,478 -chr6 49668405 rs57295760 T G 1149.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-6.101;ClippingRankSum=0.57;DB;DP=174;FS=322.757;MLEAC=1;MLEAF=0.5;MQ=47.79;MQ0=0;MQRankSum=-5.344;QD=6.61;ReadPosRankSum=-6.45;SOR=9.149;VQSLOD=-248.5;culprit=FS;GENE=CRISP2 GT:AD:DP:GQ:PL 0/1:77,96:173:99:1178,0,1978 -chr6 49676536 rs699954 C T 48.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=8.45;culprit=FS;GENE=CRISP2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 49693598 rs1068276 G A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.41;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 49693612 rs35883674 CT C 93.25 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.08;SOR=1.179;VQSLOD=8.8;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:130,9,0 -chr6 49695232 rs510770 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CRISP3 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49701439 rs1864312 C A 1555.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.745;ClippingRankSum=0.346;DB;DP=113;FS=1.849;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.795;POSITIVE_TRAIN_SITE;QD=13.77;ReadPosRankSum=1.613;SOR=0.978;VQSLOD=2.84;culprit=ReadPosRankSum;GENE=CRISP3 GT:AD:DP:GQ:PL 0/1:63,49:112:99:1584,0,2066 -chr6 49701523 rs495335 A G 1861.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.084;ClippingRankSum=-0.565;DB;DP=149;FS=0.622;MLEAC=1;MLEAF=0.5;MQ=59.85;MQ0=0;MQRankSum=-0.4;POSITIVE_TRAIN_SITE;QD=12.5;ReadPosRankSum=3.925;SOR=0.775;VQSLOD=2.06;culprit=ReadPosRankSum;GENE=CRISP3 GT:AD:DP:GQ:PL 0/1:84,65:149:99:1890,0,2674 -chr6 49703027 rs3823210 G T 73.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.231;ClippingRankSum=-0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=14.75;ReadPosRankSum=-1.231;SOR=1.022;VQSLOD=6.26;culprit=FS;GENE=CRISP3 GT:AD:DP:GQ:PL 0/1:2,3:5:72:102,0,72 -chr6 49787315 rs5876131 G GT 25.72 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=12.86;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:62,6,0 -chr6 49798102 . C CAGAG 53.7 PASS AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=4.57;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 49803370 rs1652094 A G 290.78 PASS AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.34;SOR=4.407;VQSLOD=6.61;culprit=FS;GENE=CRISP1 GT:AD:DP:GQ:PL 1/1:0,8:8:24:319,24,0 -chr6 49807422 rs7753886 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CRISP1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49815873 rs373553362 AT A 85.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.243;ClippingRankSum=-0.384;DB;DP=85;FS=2.397;MLEAC=1;MLEAF=0.5;MQ=57.35;MQ0=0;MQRankSum=1.2;QD=1.01;ReadPosRankSum=0.512;SOR=1.508;VQSLOD=1.09;culprit=MQRankSum;GENE=CRISP1 GT:AD:DP:GQ:PL 0/1:52,14:66:99:123,0,1132 -chr6 49818670 rs780782 T C 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.96;culprit=FS;GENE=CRISP1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 49835335 rs1084051 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=CRISP1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49858594 rs2153575 C T 361.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.037;ClippingRankSum=1.977;DB;DP=21;FS=4.722;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.037;POSITIVE_TRAIN_SITE;QD=17.23;ReadPosRankSum=-0.336;SOR=0.127;VQSLOD=3.26;culprit=FS GT:AD:DP:GQ:PL 0/1:7,14:21:99:390,0,186 -chr6 49913981 rs7760672 C T 1758.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.016;ClippingRankSum=0.747;DB;DP=119;FS=1.762;MLEAC=1;MLEAF=0.5;MQ=59.81;MQ0=0;MQRankSum=0.359;POSITIVE_TRAIN_SITE;QD=14.78;ReadPosRankSum=-0.178;SOR=0.963;VQSLOD=3.22;culprit=DP;GENE=DEFB133 GT:AD:DP:GQ:PL 0/1:58,61:119:99:1787,0,1869 -chr6 49917264 rs9369926 A C 219.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.074;ClippingRankSum=-1.22;DB;DP=17;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.732;POSITIVE_TRAIN_SITE;QD=12.93;ReadPosRankSum=1.317;SOR=0.425;VQSLOD=5.32;culprit=FS;GENE=DEFB133 GT:AD:DP:GQ:PL 0/1:10,7:17:99:248,0,336 -chr6 49956510 . C T 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50045305 rs1324514 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50064359 rs9395549 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50087752 rs6458721 A C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50155014 . T A 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:29:40,0,29 -chr6 50155159 rs700005 A C 44.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.37;SOR=0.693;VQSLOD=8.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:72,6,0 -chr6 50158759 rs142079970 G GT 21.73 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.87;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:58,6,0 -chr6 50164244 rs9369936 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50169217 rs148924218 C CT 19.75 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=9.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:56,6,0 -chr6 50197539 rs6910805 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50222518 rs1340844 T C 62.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.92;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 50225593 rs9349526 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50230041 rs1596084 G C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50230068 rs7756066 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50231408 rs6903689 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50261294 rs2792835 T C 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=9.19;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 50265655 rs5876165 GA G 21.73 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=10.87;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:58,6,0 -chr6 50294995 rs10637978 A ATAATT 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.39;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 50298895 rs7775569 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50325057 rs2131281 G A 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=9.1;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 50362460 rs7745382 C A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50364398 rs6930590 G T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50366720 rs7738992 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50650700 rs537362 G C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50805942 rs2817404 T G 938.77 PASS AC=2;AF=1.0;AN=2;DB;DP=23;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.99;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.85;SOR=6.358;VQSLOD=6.9;culprit=FS;GENE=TFAP2B GT:AD:DP:GQ:PL 1/1:0,23:23:69:967,69,0 -chr6 50810497 rs1569778 T C 85.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.43;SOR=2.833;VQSLOD=7.71;culprit=FS;GENE=TFAP2B GT:AD:DP:GQ:PL 1/1:0,3:3:9:113,9,0 -chr6 50811241 rs2982621 T A 306.78 PASS AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.09;SOR=4.615;VQSLOD=5.67;culprit=FS;GENE=TFAP2B GT:AD:DP:GQ:PL 1/1:0,9:9:27:335,27,0 -chr6 50812003 rs35732696 TA T 11.99 LowQual AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=4.0;SOR=2.303;GENE=TFAP2B GT:AD:DP:GQ:PL 1/1:0,2:2:6:48,6,0 -chr6 50824804 rs2817423 T A 1009.77 PASS AC=2;AF=1.0;AN=2;DB;DP=27;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.72;SOR=6.666;VQSLOD=5.96;culprit=FS;GENE=RPS17P5 GT:AD:DP:GQ:PL 1/1:0,27:27:81:1038,81,0 -chr6 50866066 rs11754505 C T 130.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.51;SOR=1.609;VQSLOD=7.49;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:158,12,0 -chr6 50880250 rs61678343 C CT 116.87 PASS AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.73;MQ0=0;QD=16.7;SOR=3.611;VQSLOD=5.12;culprit=FS;GENE=FTH1P5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:154,15,0 -chr6 50886019 rs75756982 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=36.5;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50966615 rs557411 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51003728 rs140549964 C A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=52.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51003757 . T A 62.74 PASS AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=52.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.51;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51003762 rs145721769 T A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=52.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.99;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51162298 rs1409888 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51171408 rs1327265 G A 95.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=1.179;VQSLOD=9.33;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:123,9,0 -chr6 51173538 rs2256042 G A 107.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.75;SOR=1.179;VQSLOD=8.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 51173541 rs2256041 A G 107.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.8;SOR=1.179;VQSLOD=8.71;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 51199224 rs2796913 T C 136.9 PASS AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.38;SOR=1.981;VQSLOD=6.3;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:165,15,0 -chr6 51274751 . CTT C 59.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.55;ClippingRankSum=1.3;DP=11;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.1;MQ0=0;MQRankSum=-0.937;QD=5.43;ReadPosRankSum=0.55;SOR=0.223;VQSLOD=4.67;culprit=FS GT:AD:DP:GQ:PL 0/1:3,4:7:51:97,0,51 -chr6 51317602 rs9367432 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.44;MQ0=0;QD=7.26;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51329696 rs3928895 G C 93.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.09;SOR=2.833;VQSLOD=8.17;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:121,9,0 -chr6 51339492 rs4090367 T G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51434479 rs4997737 A G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.32;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51434483 rs181171044 A T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.26;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51446475 rs2495854 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51492046 rs9474033 T G 2499.77 PASS AC=2;AF=1.0;AN=2;DB;DP=62;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.45;SOR=8.287;VQSLOD=5.75;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,62:62:99:2528,187,0 -chr6 51492164 rs9370040 T A 258.8 PASS AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.68;SOR=4.174;VQSLOD=6.27;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,7:7:21:287,21,0 -chr6 51503597 . C CAAA 667.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.313;ClippingRankSum=-1.388;DP=300;FS=6.792;MLEAC=1;MLEAF=0.5;MQ=49.95;MQ0=0;MQRankSum=-2.762;NEGATIVE_TRAIN_SITE;QD=2.23;ReadPosRankSum=-2.418;SOR=0.016;VQSLOD=-2.167;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:77,45:122:99:705,0,1544 -chr6 51512707 rs2580009 T C 944.77 PASS AC=2;AF=1.0;AN=2;DB;DP=26;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.11;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.22;SOR=6.593;VQSLOD=5.86;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,26:26:78:973,78,0 -chr6 51521787 . C A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51523739 rs115072237 T C 6637.77 PASS AC=2;AF=1.0;AN=2;DB;DP=176;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.68;SOR=2.371;VQSLOD=5.0;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,175:175:99:6666,526,0 -chr6 51551346 rs557398 T C 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=9.05;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 51590078 rs1326610 T C 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.76;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 51604677 . C T 956.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.698;ClippingRankSum=-0.058;DP=66;FS=6.929;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.341;QD=14.5;ReadPosRankSum=1.938;SOR=0.066;VQSLOD=0.46;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:36,30:66:99:985,0,1262 -chr6 51606225 rs142928645 C T 114.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.0;ClippingRankSum=-1.38;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.38;POSITIVE_TRAIN_SITE;QD=19.13;ReadPosRankSum=0.72;SOR=1.329;VQSLOD=4.76;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:2,4:6:59:143,0,59 -chr6 51611733 rs200125913 A C 194.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-2.113;ClippingRankSum=1.133;DB;DP=24;FS=9.938;MLEAC=1;MLEAF=0.5;MQ=56.04;MQ0=0;MQRankSum=-0.153;NEGATIVE_TRAIN_SITE;QD=8.12;ReadPosRankSum=0.643;SOR=3.99;VQSLOD=-1.655;culprit=QD;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:8,16:24:99:223,0,155 -chr6 51617800 rs1326607 A G 332.77 PASS AC=2;AF=1.0;AN=2;DB;DP=10;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.28;SOR=4.804;VQSLOD=6.82;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,10:10:30:361,30,0 -chr6 51634407 . T C 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51640751 rs3920621 C G 1527.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.616;ClippingRankSum=-0.475;DB;DP=114;FS=5.314;MLEAC=1;MLEAF=0.5;MQ=59.67;MQ0=0;MQRankSum=-1.12;POSITIVE_TRAIN_SITE;QD=13.4;ReadPosRankSum=-0.393;SOR=0.217;VQSLOD=1.32;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:63,49:112:99:1556,0,2311 -chr6 51649062 rs11435548 G GT 58.25 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.42;SOR=1.179;VQSLOD=7.95;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:95,9,0 -chr6 51649079 rs4715232 A G 59.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=7.4;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 51652585 rs1326561 A G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=7.54;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51652595 rs1326562 T G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.18;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51655796 rs6904634 T C 99.28 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.93;SOR=2.303;VQSLOD=6.99;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:9:127,9,0 -chr6 51655803 rs6924716 C T 99.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.09;SOR=2.833;VQSLOD=7.69;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:127,9,0 -chr6 51656236 rs7765455 G T 1483.77 PASS AC=2;AF=1.0;AN=2;DB;DP=40;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.49;SOR=3.611;VQSLOD=5.62;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,40:40:99:1512,120,0 -chr6 51656388 rs4715233 A G 93.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.09;SOR=2.833;VQSLOD=8.93;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:121,9,0 -chr6 51664791 rs1980834 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51664816 rs2148459 T G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51671321 rs1326584 T A 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=7.93;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 51671350 rs4470847 C G 66.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.09;SOR=1.179;VQSLOD=9.01;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:94,9,0 -chr6 51673939 rs1326588 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51706167 rs10648630 C CCCTTT 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.9;SOR=0.693;VQSLOD=8.28;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51712492 rs9370067 A T 1705.77 PASS AC=2;AF=1.0;AN=2;DB;DP=42;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.14;SOR=7.523;VQSLOD=6.66;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,42:42:99:1734,126,0 -chr6 51718857 rs1831015 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51720838 rs9349603 T C 7371.77 PASS AC=2;AF=1.0;AN=2;DB;DP=189;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.82;SOR=2.858;VQSLOD=4.99;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,185:185:99:7400,557,0 -chr6 51720872 rs7452724 A G 6199.77 PASS AC=2;AF=1.0;AN=2;DB;DP=161;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.66;SOR=3.188;VQSLOD=6.56;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,161:161:99:6228,484,0 -chr6 51723015 rs9370074 G A 50.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=2.303;VQSLOD=7.56;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 51732598 rs9382043 G A 2712.77 PASS AC=2;AF=1.0;AN=2;DB;DP=74;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.5;SOR=3.026;VQSLOD=5.85;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,74:74:99:2741,222,0 -chr6 51732628 rs9382044 G A 3330.77 PASS AC=2;AF=1.0;AN=2;DB;DP=89;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.74;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.8;SOR=2.276;VQSLOD=6.28;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,89:89:99:3359,267,0 -chr6 51735261 rs982874 G T 2752.77 PASS AC=2;AF=1.0;AN=2;DB;DP=73;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.49;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.4;SOR=4.558;VQSLOD=6.0;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2781,220,0 -chr6 51735613 rs2064871 T C 314.78 PASS AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.95;SOR=4.407;VQSLOD=6.77;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,8:8:24:343,24,0 -chr6 51747589 rs6458801 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51750563 rs4711985 A T 498.77 PASS AC=2;AF=1.0;AN=2;DB;DP=13;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.32;SOR=5.283;VQSLOD=6.36;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,13:13:39:527,39,0 -chr6 51757014 rs1321516 C T 63.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.44;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 51768630 rs141063789 CATATAT C 229.77 PASS AC=2;AF=1.0;AN=2;DB;DP=22;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=56.71;MQ0=0;POSITIVE_TRAIN_SITE;QD=10.44;SOR=2.303;VQSLOD=6.39;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,6:6:20:267,20,0 -chr6 51791091 rs4711990 G T 63.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.23;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 51793425 rs5876244 C CA 44.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=0.693;VQSLOD=8.4;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 51796751 rs3857602 G A 89.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.76;SOR=1.179;VQSLOD=5.58;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:117,9,0 -chr6 51798753 rs1266888 G A 308.78 PASS AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.9;SOR=4.407;VQSLOD=6.3;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,8:8:24:337,24,0 -chr6 51798760 rs1884953 T A 94.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.0;ClippingRankSum=-0.365;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.365;POSITIVE_TRAIN_SITE;QD=9.48;ReadPosRankSum=-0.365;SOR=0.412;VQSLOD=6.15;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:6,4:10:99:123,0,204 -chr6 51799166 rs1266889 T C 1497.77 PASS AC=2;AF=1.0;AN=2;DB;DP=38;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.26;SOR=4.977;VQSLOD=5.51;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,37:37:99:1526,111,0 -chr6 51800445 rs1266890 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51814216 rs4715264 C T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.34;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51814217 rs1266913 A G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.56;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51844368 rs2435324 A G 48.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=8.63;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 51856374 rs9463746 A G 45.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=2.303;VQSLOD=8.12;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 -chr6 51875250 rs2435322 A C 4902.77 PASS AC=2;AF=1.0;AN=2;DB;DP=132;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.68;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.79;SOR=1.17;VQSLOD=5.57;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,130:130:99:4931,391,0 -chr6 51882075 rs9349614 C G 29.77 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=1.067;ClippingRankSum=0.572;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.589;QD=3.31;ReadPosRankSum=0.572;SOR=0.169;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:6,2:8:58:58,0,201 -chr6 51889483 rs45517932 G A 1402.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.623;ClippingRankSum=-0.441;DB;DP=91;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.758;QD=15.42;ReadPosRankSum=0.099;SOR=0.684;VQSLOD=3.39;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:47,44:91:99:1431,0,1559 -chr6 51890823 rs9296669 G A 908.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.796;ClippingRankSum=-1.279;DB;DP=60;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.45;MQ0=0;MQRankSum=0.614;POSITIVE_TRAIN_SITE;QD=15.15;ReadPosRankSum=0.052;SOR=0.575;VQSLOD=5.85;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:30,30:60:99:937,0,937 -chr6 51891011 rs2499480 T C 1469.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.48;ClippingRankSum=1.669;DB;DP=99;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.53;MQ0=0;MQRankSum=-0.671;POSITIVE_TRAIN_SITE;QD=14.85;ReadPosRankSum=0.425;SOR=0.787;VQSLOD=5.12;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:54,45:99:99:1498,0,1703 -chr6 51913240 rs10948667 G A 2227.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.872;ClippingRankSum=0.978;DB;DP=133;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.127;POSITIVE_TRAIN_SITE;QD=16.75;ReadPosRankSum=0.314;SOR=0.691;VQSLOD=4.01;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:61,72:133:99:2256,0,2006 -chr6 51914898 rs9395759 T C 962.77 PASS AC=2;AF=1.0;AN=2;DB;DP=27;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=54.65;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.45;SOR=5.211;VQSLOD=6.92;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,27:27:81:991,81,0 -chr6 51914956 rs9370096 G A 738.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.924;ClippingRankSum=-1.239;DB;DP=57;FS=1.721;MLEAC=1;MLEAF=0.5;MQ=53.16;MQ0=0;MQRankSum=-2.997;POSITIVE_TRAIN_SITE;QD=12.96;ReadPosRankSum=0.567;SOR=1.274;VQSLOD=0.74;culprit=MQRankSum;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:30,27:57:99:767,0,838 -chr6 51917550 rs1896983 G A 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.73;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 51923569 rs56342114 CTCTA C 188.84 PASS AC=2;AF=1.0;AN=2;DB;DP=12;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.74;SOR=3.611;VQSLOD=5.56;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,5:5:16:226,16,0 -chr6 51924774 rs1896976 A G 11214.77 PASS AC=2;AF=1.0;AN=2;DB;DP=307;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.86;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.73;SOR=0.923;VQSLOD=3.9;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,306:306:99:11243,918,0 -chr6 51927683 rs13198604 T C 130.79 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=21.8;ReadPosRankSum=0.736;SOR=0.941;VQSLOD=5.66;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:1,5:6:22:159,0,22 -chr6 51930886 rs5876252 T TA 1123.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.558;ClippingRankSum=0.596;DB;DP=98;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.11;MQ0=0;MQRankSum=0.066;POSITIVE_TRAIN_SITE;QD=11.47;ReadPosRankSum=0.047;SOR=1.571;VQSLOD=5.61;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:14,49:63:99:1161,0,109 -chr6 51935061 rs4711996 T G 632.77 PASS AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.75;SOR=5.67;VQSLOD=6.32;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,16:16:48:661,48,0 -chr6 51935747 rs17576809 C T 1555.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.681;ClippingRankSum=0.579;DB;DP=78;FS=1.884;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.207;POSITIVE_TRAIN_SITE;QD=19.95;ReadPosRankSum=2.282;SOR=1.437;VQSLOD=1.66;culprit=ReadPosRankSum;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:34,44:78:99:1584,0,1003 -chr6 51936846 rs3936986 T C 1197.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.52;ClippingRankSum=2.065;DB;DP=65;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.65;MQ0=0;MQRankSum=-0.165;POSITIVE_TRAIN_SITE;QD=18.43;ReadPosRankSum=-0.31;SOR=0.499;VQSLOD=5.41;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:29,36:65:99:1226,0,894 -chr6 51938242 rs9474140 A G 2915.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=5.879;ClippingRankSum=-1.66;DB;DP=204;FS=1.266;MLEAC=1;MLEAF=0.5;MQ=59.55;MQ0=0;MQRankSum=0.616;POSITIVE_TRAIN_SITE;QD=14.29;ReadPosRankSum=0.116;SOR=0.846;VQSLOD=2.35;culprit=DP;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:112,92:204:99:2944,0,3367 -chr6 51944847 rs1892274 T C 1304.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.941;ClippingRankSum=0.488;DB;DP=91;FS=6.922;MLEAC=1;MLEAF=0.5;MQ=59.75;MQ0=0;MQRankSum=-0.933;POSITIVE_TRAIN_SITE;QD=14.34;ReadPosRankSum=0.242;SOR=2.14;VQSLOD=2.08;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:45,46:91:99:1333,0,1431 -chr6 51946893 rs6458806 T C 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=8.64;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 51947237 rs9474143 G A 5131.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.494;ClippingRankSum=0.221;DB;DP=273;FS=2.813;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.398;POSITIVE_TRAIN_SITE;QD=18.8;ReadPosRankSum=1.871;SOR=0.538;VQSLOD=1.29;culprit=DP;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:114,158:272:99:5160,0,3305 -chr6 51949862 rs9370097 A G 953.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.068;ClippingRankSum=-1.115;DB;DP=65;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.363;POSITIVE_TRAIN_SITE;QD=14.67;ReadPosRankSum=-0.917;SOR=0.505;VQSLOD=5.49;culprit=FS;GENE=PKHD1 GT:AD:DP:GQ:PL 0/1:36,29:65:99:982,0,1231 -chr6 51953191 rs6905678 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51963443 rs6914462 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51971195 rs3997006 T C 91.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=2.833;VQSLOD=7.51;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:119,9,0 -chr6 51997155 rs1892278 A C 327.78 PASS AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.88;SOR=3.056;VQSLOD=5.59;culprit=FS GT:AD:DP:GQ:PL 1/1:0,9:9:27:356,27,0 -chr6 52054249 rs7747909 G A 105.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.421;ClippingRankSum=0.922;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.017;POSITIVE_TRAIN_SITE;QD=13.22;ReadPosRankSum=0.0;SOR=0.693;VQSLOD=4.45;culprit=FS;GENE=IL17A GT:AD:DP:GQ:PL 0/1:4,4:8:99:134,0,134 -chr6 52061133 rs11962054 A G 16.63 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=16.63;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:43,3,0 -chr6 52064989 rs11755816 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52065009 rs11751159 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52073500 rs4464776 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52075816 rs2397079 A G 59.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=9.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 52085748 rs591274 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52111808 rs761167 C T 630.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.571;ClippingRankSum=-0.018;DB;DP=33;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.3;MQ0=0;MQRankSum=0.792;POSITIVE_TRAIN_SITE;QD=19.11;ReadPosRankSum=0.534;SOR=0.743;VQSLOD=5.64;culprit=FS;GENE=SLC25A20P1 GT:AD:DP:GQ:PL 0/1:13,20:33:99:659,0,402 -chr6 52117224 rs604952 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52129484 rs2230240 C T 3990.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.023;ClippingRankSum=-0.723;DB;DP=236;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.012;POSITIVE_TRAIN_SITE;QD=16.91;ReadPosRankSum=2.682;SOR=0.712;VQSLOD=1.85;culprit=FS;GENE=MCM3 GT:AD:DP:GQ:PL 0/1:105,131:236:99:4019,0,2992 -chr6 52129667 rs2307326 G A 917.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.356;ClippingRankSum=-0.312;DB;DP=53;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.791;POSITIVE_TRAIN_SITE;QD=17.32;ReadPosRankSum=-2.147;SOR=0.808;VQSLOD=3.93;culprit=ReadPosRankSum;GENE=MCM3 GT:AD:DP:GQ:PL 0/1:25,28:53:99:946,0,873 -chr6 52130745 rs6925229 T C 162.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.139;ClippingRankSum=1.898;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.488;POSITIVE_TRAIN_SITE;QD=10.17;ReadPosRankSum=0.597;SOR=0.34;VQSLOD=6.23;culprit=FS;GENE=MCM3 GT:AD:DP:GQ:PL 0/1:10,6:16:99:191,0,354 -chr6 52131254 rs10807441 C T 1383.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.953;ClippingRankSum=0.77;DB;DP=83;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.223;POSITIVE_TRAIN_SITE;QD=16.67;ReadPosRankSum=0.269;SOR=1.534;VQSLOD=5.05;culprit=FS;GENE=MCM3 GT:AD:DP:GQ:PL 0/1:43,40:83:99:1412,0,1442 -chr6 52137313 rs12207056 C T 464.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.684;ClippingRankSum=-0.306;DB;DP=33;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=47.56;MQ0=0;MQRankSum=-0.162;POSITIVE_TRAIN_SITE;QD=14.08;ReadPosRankSum=1.207;SOR=1.609;VQSLOD=5.72;culprit=FS;GENE=MCM3 GT:AD:DP:GQ:PL 0/1:17,16:33:99:493,0,518 -chr6 52138441 rs6918669 G A 286.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.355;ClippingRankSum=-0.442;DB;DP=18;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=15.93;ReadPosRankSum=0.971;SOR=1.781;VQSLOD=6.47;culprit=FS;GENE=MCM3 GT:AD:DP:GQ:PL 0/1:9,9:18:99:315,0,267 -chr6 52141670 rs3765446 A T 142.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.635;ClippingRankSum=1.0;DB;DP=12;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.134;POSITIVE_TRAIN_SITE;QD=11.9;ReadPosRankSum=0.135;SOR=1.371;VQSLOD=6.12;culprit=FS;GENE=MCM3 GT:AD:DP:GQ:PL 0/1:7,5:12:99:171,0,247 -chr6 52142092 rs2307325 C T 222.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.092;ClippingRankSum=0.092;DB;DP=24;FS=1.999;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.276;POSITIVE_TRAIN_SITE;QD=9.28;ReadPosRankSum=0.704;SOR=1.214;VQSLOD=2.73;culprit=QD;GENE=MCM3 GT:AD:DP:GQ:PL 0/1:16,8:24:99:251,0,540 -chr6 52142582 rs13191372 G A 424.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.394;ClippingRankSum=0.496;DB;DP=31;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.5;MQ0=0;MQRankSum=0.695;POSITIVE_TRAIN_SITE;QD=13.7;ReadPosRankSum=1.409;SOR=0.527;VQSLOD=5.12;culprit=FS;GENE=MCM3 GT:AD:DP:GQ:PL 0/1:17,14:31:99:453,0,593 -chr6 52143987 rs2076510 C T 232.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.78;ClippingRankSum=-0.625;DB;DP=17;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.241;POSITIVE_TRAIN_SITE;QD=13.69;ReadPosRankSum=1.973;SOR=0.593;VQSLOD=5.87;culprit=FS;GENE=MCM3 GT:AD:DP:GQ:PL 0/1:9,8:17:99:261,0,314 -chr6 52144081 rs2073036 T C 952.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.283;ClippingRankSum=-0.724;DB;DP=63;FS=1.092;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.193;POSITIVE_TRAIN_SITE;QD=15.12;ReadPosRankSum=0.145;SOR=0.485;VQSLOD=2.82;culprit=FS;GENE=MCM3 GT:AD:DP:GQ:PL 0/1:29,34:63:99:981,0,911 -chr6 52147271 rs7756989 T C 20.8 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.72;ClippingRankSum=1.38;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.72;QD=3.47;ReadPosRankSum=0.72;SOR=0.693;GENE=MCM3 GT:AD:DP:GQ:PL 0/1:4,2:6:49:49,0,109 -chr6 52147363 rs12202495 A G 191.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.279;ClippingRankSum=0.579;DB;DP=20;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.193;POSITIVE_TRAIN_SITE;QD=9.59;ReadPosRankSum=1.042;SOR=0.392;VQSLOD=5.45;culprit=FS;GENE=MCM3 GT:AD:DP:GQ:PL 0/1:12,8:20:99:220,0,424 -chr6 52147692 rs2307322 T A 893.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=5.042;ClippingRankSum=0.16;DB;DP=47;FS=9.107;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.46;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=19.02;ReadPosRankSum=3.166;SOR=2.472;VQSLOD=0.472;culprit=ReadPosRankSum;GENE=MCM3 GT:AD:DP:GQ:PL 0/1:22,25:47:99:922,0,588 -chr6 52148465 rs9474192 T G 63.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.21;culprit=QD;GENE=MCM3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 52217185 rs9395785 C G 142.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-0.922;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.495;POSITIVE_TRAIN_SITE;QD=20.4;ReadPosRankSum=0.922;SOR=1.609;VQSLOD=5.94;culprit=FS GT:AD:DP:GQ:PL 0/1:2,5:7:66:171,0,66 -chr6 52240487 rs6458837 G A 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=7.88;culprit=FS;GENE=PAQR8 GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 52245945 rs71794438 CA C 38.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=2.303;VQSLOD=7.53;culprit=FS;GENE=PAQR8 GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 52257835 rs669893 A G 17.61 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=17.61;SOR=1.609;GENE=PAQR8 GT:AD:DP:GQ:PL 1/1:0,1:1:3:44,3,0 -chr6 52257856 rs526553 G C 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.49;culprit=FS;GENE=PAQR8 GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 52267967 rs76408349 A C 39.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=1.231;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.21;MQ0=0;MQRankSum=1.231;POSITIVE_TRAIN_SITE;QD=7.95;ReadPosRankSum=-0.358;SOR=0.446;VQSLOD=5.7;culprit=QD;GENE=PAQR8 GT:AD:DP:GQ:PL 0/1:3,2:5:68:68,0,92 -chr6 52268008 rs3748066 T G 117.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.495;ClippingRankSum=0.198;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.03;MQ0=0;MQRankSum=-0.922;POSITIVE_TRAIN_SITE;QD=16.82;ReadPosRankSum=-0.922;SOR=0.527;VQSLOD=6.33;culprit=FS;GENE=PAQR8 GT:AD:DP:GQ:PL 0/1:2,5:7:62:146,0,62 -chr6 52268086 rs146353145 C T 319.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.458;ClippingRankSum=-0.387;DB;DP=21;FS=3.222;MLEAC=1;MLEAF=0.5;MQ=57.77;MQ0=0;MQRankSum=-0.81;QD=15.23;ReadPosRankSum=0.599;SOR=1.911;VQSLOD=1.55;culprit=FS;GENE=PAQR8 GT:AD:DP:GQ:PL 0/1:10,11:21:99:348,0,301 -chr6 52268890 rs17591381 G A 546.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.06;ClippingRankSum=0.774;DB;DP=49;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.58;MQ0=0;MQRankSum=1.035;POSITIVE_TRAIN_SITE;QD=11.16;ReadPosRankSum=0.794;SOR=0.712;VQSLOD=5.57;culprit=FS;GENE=PAQR8 GT:AD:DP:GQ:PL 0/1:27,22:49:99:575,0,819 -chr6 52269199 rs3799272 T C 59.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=9.07;culprit=FS;GENE=PAQR8 GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 52296461 rs1840169 G C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EFHC1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52319251 rs614570 C T 274.18 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.751;ClippingRankSum=0.751;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.751;POSITIVE_TRAIN_SITE;QD=30.46;ReadPosRankSum=0.751;SOR=3.056;VQSLOD=5.38;culprit=FS;GENE=EFHC1 GT:AD:DP:GQ:PL 0/1:1,8:9:10:302,0,10 -chr6 52355206 rs2273120 T C 1095.77 PASS AC=2;AF=1.0;AN=2;DB;DP=30;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.61;SOR=5.353;VQSLOD=6.99;culprit=FS;GENE=EFHC1 GT:AD:DP:GQ:PL 1/1:0,29:29:87:1124,87,0 -chr6 52357260 rs7757370 C A 601.77 PASS AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.84;SOR=5.67;VQSLOD=6.12;culprit=FS;GENE=EFHC1 GT:AD:DP:GQ:PL 1/1:0,16:16:48:630,48,0 -chr6 52367845 rs3032 C T 381.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.028;ClippingRankSum=0.927;DB;DP=24;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.03;MQ0=0;MQRankSum=0.695;POSITIVE_TRAIN_SITE;QD=15.91;ReadPosRankSum=-0.348;SOR=0.859;VQSLOD=5.92;culprit=FS;GENE=EFHC1,TRAM2 GT:AD:DP:GQ:PL 0/1:11,13:24:99:410,0,338 -chr6 52370939 rs9688915 G A 1148.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.52;ClippingRankSum=1.052;DB;DP=64;FS=1.426;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.175;POSITIVE_TRAIN_SITE;QD=17.95;ReadPosRankSum=0.836;SOR=1.212;VQSLOD=2.7;culprit=ReadPosRankSum;GENE=EFHC1,TRAM2 GT:AD:DP:GQ:PL 0/1:29,35:64:99:1177,0,853 -chr6 52380641 rs941968 C T 424.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.39;ClippingRankSum=-1.102;DB;DP=30;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.395;POSITIVE_TRAIN_SITE;QD=14.16;ReadPosRankSum=0.603;SOR=0.576;VQSLOD=5.79;culprit=FS;GENE=EFHC1,TRAM2 GT:AD:DP:GQ:PL 0/1:16,14:30:99:453,0,559 -chr6 52381728 rs6917085 A T 86.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=21.69;ReadPosRankSum=-0.727;SOR=1.609;VQSLOD=6.1;culprit=FS;GENE=EFHC1,TRAM2 GT:AD:DP:GQ:PL 0/1:1,3:4:32:115,0,32 -chr6 52425189 rs7744675 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=TRAM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52433894 rs55959984 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=TRAM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52451301 . A G 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52453985 rs9370135 T A 42.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.26;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.69;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:30:71,0,30 -chr6 52469904 rs9463802 A G 49.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=9.2;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 52475696 . C A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52483058 rs11755043 C A 49.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=8.1;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 52538160 rs55704840 A AG 38.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=0.693;VQSLOD=8.83;culprit=FS;GENE=TMEM14A GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 52538171 rs7746344 A G 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.58;culprit=FS;GENE=TMEM14A GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 52538198 rs9349638 T A 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.37;SOR=0.693;VQSLOD=7.1;culprit=FS;GENE=TMEM14A GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 52538242 rs9349639 T G 50.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=0.693;VQSLOD=7.79;culprit=FS;GENE=TMEM14A GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 52538390 rs9349640 T C 45.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=0.693;VQSLOD=8.54;culprit=FS;GENE=TMEM14A GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 -chr6 52541811 rs13211066 G A 2092.77 PASS AC=2;AF=1.0;AN=2;DB;DP=52;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.36;SOR=7.941;VQSLOD=6.16;culprit=FS;GENE=TMEM14A GT:AD:DP:GQ:PL 1/1:0,52:52:99:2121,157,0 -chr6 52546789 rs2281484 C T 1421.77 PASS AC=2;AF=1.0;AN=2;DB;DP=38;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.25;SOR=7.328;VQSLOD=7.46;culprit=FS;GENE=TMEM14A GT:AD:DP:GQ:PL 1/1:0,38:38:99:1450,114,0 -chr6 52553436 rs9382133 C T 766.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.752;ClippingRankSum=0.06;DB;DP=45;FS=4.452;MLEAC=1;MLEAF=0.5;MQ=58.55;MQ0=0;MQRankSum=0.37;POSITIVE_TRAIN_SITE;QD=17.04;ReadPosRankSum=0.418;SOR=1.118;VQSLOD=2.96;culprit=FS;GENE=GSTA8P GT:AD:DP:GQ:PL 0/1:18,26:44:99:795,0,532 -chr6 52565427 rs4637643 T G 63.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.3;culprit=FS;GENE=GSTA8P GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 52568775 rs6909894 G C 181.9 PASS AC=2;AF=1.0;AN=2;DB;DP=6;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.32;SOR=1.981;VQSLOD=6.47;culprit=FS;GENE=GSTA8P GT:AD:DP:GQ:PL 1/1:0,5:5:15:210,15,0 -chr6 52568848 rs36098646 G GA 25.95 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=62.65;MQ0=0;MQRankSum=0.727;QD=6.49;ReadPosRankSum=0.727;SOR=0.916;GENE=GSTA8P GT:AD:DP:GQ:PL 0/1:1,3:4:13:63,0,13 -chr6 52615371 rs199546282 T G 302.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-7.16;ClippingRankSum=-0.23;DB;DP=163;FS=296.91;MLEAC=1;MLEAF=0.5;MQ=54.98;MQ0=0;MQRankSum=-0.947;QD=1.86;ReadPosRankSum=-4.824;SOR=8.189;VQSLOD=-199.5;culprit=FS;GENE=GSTA2 GT:AD:DP:GQ:PL 0/1:103,59:162:99:331,0,2945 -chr6 52616633 rs72934249 C T 667.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.954;ClippingRankSum=0.781;DB;DP=47;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.51;MQ0=0;MQRankSum=0.909;POSITIVE_TRAIN_SITE;QD=14.21;ReadPosRankSum=-0.631;SOR=0.509;VQSLOD=5.18;culprit=FS;GENE=GSTA2 GT:AD:DP:GQ:PL 0/1:26,21:47:99:696,0,789 -chr6 52617731 rs2180314 C G 6239.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.736;ClippingRankSum=-0.69;DB;DP=405;FS=1.2;MLEAC=1;MLEAF=0.5;MQ=59.74;MQ0=0;MQRankSum=-0.793;POSITIVE_TRAIN_SITE;QD=15.41;ReadPosRankSum=1.185;SOR=0.583;VQSLOD=1.22;culprit=DP;GENE=GSTA2 GT:AD:DP:GQ:PL 0/1:207,197:404:99:6268,0,6969 -chr6 52622475 rs2608624 G T 277.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.387;ClippingRankSum=-0.529;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.529;POSITIVE_TRAIN_SITE;QD=17.36;ReadPosRankSum=-1.482;SOR=0.941;VQSLOD=4.88;culprit=FS;GENE=GSTA2 GT:AD:DP:GQ:PL 0/1:7,9:16:99:306,0,255 -chr6 52622814 rs2254050 C T 889.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=5.466;ClippingRankSum=2.068;DB;DP=50;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.456;POSITIVE_TRAIN_SITE;QD=17.8;ReadPosRankSum=0.651;SOR=0.773;VQSLOD=5.34;culprit=FS;GENE=GSTA2 GT:AD:DP:GQ:PL 0/1:24,26:50:99:918,0,713 -chr6 52630153 rs6458868 C T 560.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.03;ClippingRankSum=-0.43;DB;DP=42;FS=1.283;MLEAC=1;MLEAF=0.5;MQ=56.17;MQ0=0;MQRankSum=0.483;POSITIVE_TRAIN_SITE;QD=13.35;ReadPosRankSum=2.308;SOR=1.064;VQSLOD=2.33;culprit=ReadPosRankSum;GENE=GSTA12P GT:AD:DP:GQ:PL 0/1:21,20:41:99:589,0,560 -chr6 52630269 rs6458869 C A 534.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.861;ClippingRankSum=-1.139;DB;DP=26;FS=1.757;MLEAC=1;MLEAF=0.5;MQ=49.59;MQ0=0;MQRankSum=-2.083;POSITIVE_TRAIN_SITE;QD=20.57;ReadPosRankSum=-0.583;SOR=0.346;VQSLOD=1.61;culprit=MQRankSum;GENE=GSTA12P GT:AD:DP:GQ:PL 0/1:8,18:26:99:563,0,197 -chr6 52631188 rs2749029 A G 696.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.911;ClippingRankSum=0.581;DB;DP=58;FS=2.243;MLEAC=1;MLEAF=0.5;MQ=59.68;MQ0=0;MQRankSum=-0.722;POSITIVE_TRAIN_SITE;QD=12.01;ReadPosRankSum=0.581;SOR=0.416;VQSLOD=2.99;culprit=QD;GENE=GSTA12P GT:AD:DP:GQ:PL 0/1:33,25:58:99:725,0,1078 -chr6 52655827 rs6904269 G A 49.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=9.25;culprit=FS;GENE=GSTA1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 52657321 rs4147615 T C 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=9.21;culprit=DP;GENE=GSTA1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 52658962 rs1051775 T C 16388.77 VQSRTrancheSNP99.00to99.90 AC=2;AF=1.0;AN=2;BaseQRankSum=1.724;ClippingRankSum=-0.564;DB;DP=430;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.91;MQ0=0;MQRankSum=0.177;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=26.2;ReadPosRankSum=0.878;SOR=0.736;VQSLOD=-0.8417;culprit=DP;GENE=GSTA1 GT:AD:DP:GQ:PL 1/1:1,429:430:99:16417,1283,0 -chr6 52660828 rs2894803 C A 2866.77 PASS AC=2;AF=1.0;AN=2;DB;DP=74;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=56.91;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.82;SOR=8.608;VQSLOD=6.77;culprit=FS;GENE=GSTA1 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2895,220,0 -chr6 52661267 . ATATATATATATATATATATATGTGTG A 235.79 PASS AC=2;AF=1.0;AN=2;DP=21;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=43.56;MQ0=0;QD=11.23;SOR=3.912;VQSLOD=4.84;culprit=FS;GENE=GSTA1 GT:AD:DP:GQ:PL 1/1:0,6:6:19:273,19,0 -chr6 52662263 rs2397106 C T 1326.77 PASS AC=2;AF=1.0;AN=2;DB;DP=39;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=41.5;MQ0=0;QD=34.02;SOR=5.892;VQSLOD=5.23;culprit=FS;GENE=GSTA1 GT:AD:DP:GQ:PL 1/1:0,38:38:99:1355,114,0 -chr6 52662568 rs139503836 G A 365.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.392;ClippingRankSum=-0.198;DB;DP=36;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.74;MQ0=0;MQRankSum=-1.778;QD=10.16;ReadPosRankSum=1.12;SOR=0.293;VQSLOD=2.34;culprit=FS;GENE=GSTA1 GT:AD:DP:GQ:PL 0/1:23,13:36:99:394,0,797 -chr6 52663705 rs9349644 C T 48.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=7.95;culprit=FS;GENE=GSTA1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 52663813 rs10948722 A G 801.77 PASS AC=2;AF=1.0;AN=2;DB;DP=20;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.84;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.88;SOR=6.091;VQSLOD=6.69;culprit=FS;GENE=GSTA1 GT:AD:DP:GQ:PL 1/1:0,20:20:60:830,60,0 -chr6 52664133 . T C 1090.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.013;ClippingRankSum=-0.873;DP=57;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.328;QD=19.14;ReadPosRankSum=0.377;SOR=0.285;VQSLOD=3.89;culprit=FS;GENE=GSTA1 GT:AD:DP:GQ:PL 0/1:26,31:57:99:1119,0,874 -chr6 52670630 rs10807454 A C 691.77 PASS AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=44.81;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.23;SOR=3.258;VQSLOD=6.57;culprit=FS;GENE=GSTA6P GT:AD:DP:GQ:PL 1/1:0,16:16:48:720,48,0 -chr6 52670633 rs62412861 A G 725.77 PASS AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=44.81;MQ0=0;QD=24.12;SOR=3.258;VQSLOD=4.49;culprit=FS;GENE=GSTA6P GT:AD:DP:GQ:PL 1/1:0,16:16:51:754,51,0 -chr6 52670639 rs62412870 C T 680.77 PASS AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=44.44;MQ0=0;QD=29.35;SOR=3.258;VQSLOD=4.94;culprit=FS;GENE=GSTA6P GT:AD:DP:GQ:PL 1/1:0,16:16:48:709,48,0 -chr6 52677230 rs5876288 G GA 2040.73 PASS AC=2;AF=1.0;AN=2;BaseQRankSum=-0.42;ClippingRankSum=0.166;DB;DP=129;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.66;MQ0=0;MQRankSum=0.381;POSITIVE_TRAIN_SITE;QD=15.82;ReadPosRankSum=-0.674;SOR=1.636;VQSLOD=4.43;culprit=FS;GENE=GSTA6P GT:AD:DP:GQ:PL 1/1:6,81:87:99:2070,156,0 -chr6 52678337 rs6458873 G T 1706.77 PASS AC=2;AF=1.0;AN=2;DB;DP=44;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.48;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.61;SOR=5.33;VQSLOD=6.87;culprit=FS;GENE=GSTA6P GT:AD:DP:GQ:PL 1/1:0,44:44:99:1735,132,0 -chr6 52678463 rs6458874 C T 360.77 PASS AC=2;AF=1.0;AN=2;DB;DP=10;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.66;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.2;SOR=4.804;VQSLOD=6.59;culprit=FS;GENE=GSTA6P GT:AD:DP:GQ:PL 1/1:0,10:10:30:389,30,0 -chr6 52678500 rs6458875 C G 82.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.43;SOR=2.833;VQSLOD=8.62;culprit=FS;GENE=GSTA6P GT:AD:DP:GQ:PL 1/1:0,3:3:9:110,9,0 -chr6 52688905 rs2983232 G T 13.72 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=13.72;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 -chr6 52694086 rs4311507 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52695461 rs10948726 G T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=36.5;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52697601 rs55815585 T G 3617.77 PASS AC=2;AF=1.0;AN=2;DB;DP=94;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.68;SOR=2.354;VQSLOD=5.15;culprit=FS;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,92:92:99:3646,277,0 -chr6 52697825 rs4715345 A C 5351.77 PASS AC=2;AF=1.0;AN=2;DB;DP=123;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.29;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.62;SOR=2.226;VQSLOD=5.04;culprit=FS;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,122:122:99:5380,367,0 -chr6 52697834 rs4715346 C A 5365.77 PASS AC=2;AF=1.0;AN=2;DB;DP=120;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.25;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.36;SOR=2.507;VQSLOD=5.69;culprit=FS;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,120:120:99:5394,370,0 -chr6 52697890 rs4715347 C T 2514.77 PASS AC=2;AF=1.0;AN=2;DB;DP=66;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.18;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.91;SOR=5.042;VQSLOD=6.95;culprit=QD;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,65:65:99:2543,195,0 -chr6 52698035 rs4715348 A G 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=8.47;culprit=FS;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 52698653 rs6458880 C T 131.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.76;SOR=3.258;VQSLOD=7.46;culprit=FS;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,4:4:12:159,12,0 -chr6 52698788 rs4712021 T C 3962.77 PASS AC=2;AF=1.0;AN=2;DB;DP=88;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.48;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.39;SOR=8.977;VQSLOD=6.17;culprit=FS;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,88:88:99:3991,271,0 -chr6 52698798 rs4715349 G T 4293.77 PASS AC=2;AF=1.0;AN=2;DB;DP=99;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.06;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.88;SOR=9.21;VQSLOD=6.95;culprit=DP;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,99:99:99:4322,298,0 -chr6 52700920 rs2397117 T C 5074.77 PASS AC=2;AF=1.0;AN=2;DB;DP=131;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.86;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.54;SOR=9.735;VQSLOD=6.59;culprit=FS;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,129:129:99:5103,388,0 -chr6 52701143 rs2397118 C T 12265.77 PASS AC=2;AF=1.0;AN=2;DB;DP=338;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.8;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.4;SOR=1.526;VQSLOD=2.73;culprit=FS;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,337:337:99:12294,1013,0 -chr6 52701458 rs2397119 T C 81.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.09;SOR=2.833;VQSLOD=7.99;culprit=FS;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,3:3:9:109,9,0 -chr6 52701582 rs62412887 T A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.25;culprit=FS;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 52701589 rs2397121 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=7.15;culprit=FS;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 52702324 rs4715350 T C 4926.77 PASS AC=2;AF=1.0;AN=2;DB;DP=136;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.3;SOR=3.048;VQSLOD=4.71;culprit=FS;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,135:135:99:4955,406,0 -chr6 52702529 rs4715351 T C 1973.77 PASS AC=2;AF=1.0;AN=2;DB;DP=48;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.52;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.8;SOR=7.743;VQSLOD=6.84;culprit=FS;GENE=GSTA5 GT:AD:DP:GQ:PL 1/1:0,47:47:99:2002,141,0 -chr6 52712461 rs9296693 G A 232.8 PASS AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.26;SOR=4.174;VQSLOD=3.81;culprit=FS;GENE=GSTA11P GT:AD:DP:GQ:PL 1/1:0,7:7:21:261,21,0 -chr6 52712645 rs9296694 C G 4081.77 PASS AC=2;AF=1.0;AN=2;DB;DP=107;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.14;SOR=2.812;VQSLOD=6.01;culprit=FS;GENE=GSTA11P GT:AD:DP:GQ:PL 1/1:0,107:107:99:4110,322,0 -chr6 52713902 rs62412891 C T 1799.77 PASS AC=2;AF=1.0;AN=2;DB;DP=47;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.94;SOR=3.958;VQSLOD=6.18;culprit=FS;GENE=GSTA11P GT:AD:DP:GQ:PL 1/1:0,47:47:99:1828,141,0 -chr6 52724654 rs9349647 C T 94.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=2.833;VQSLOD=8.25;culprit=FS;GENE=GSTA11P GT:AD:DP:GQ:PL 1/1:0,3:3:9:122,9,0 -chr6 52735179 rs72938158 T A 2626.77 PASS AC=2;AF=1.0;AN=2;BaseQRankSum=1.785;ClippingRankSum=1.186;DB;DP=68;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;MQRankSum=-1.577;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=31.32;ReadPosRankSum=3.323;SOR=5.136;VQSLOD=0.542;culprit=ReadPosRankSum;GENE=GSTA11P GT:AD:DP:GQ:PL 1/1:4,64:68:99:2655,186,0 -chr6 52743455 rs4715360 T C 2478.77 PASS AC=2;AF=1.0;AN=2;DB;DP=62;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=8.287;VQSLOD=5.41;culprit=FS;GENE=GSTA10P GT:AD:DP:GQ:PL 1/1:0,62:62:99:2507,187,0 -chr6 52744741 rs13198332 G A 498.77 PASS AC=2;AF=1.0;AN=2;DB;DP=14;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.93;SOR=0.693;VQSLOD=6.43;culprit=FS;GENE=GSTA10P GT:AD:DP:GQ:PL 1/1:0,14:14:42:527,42,0 -chr6 52746642 rs72940404 G A 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:30:40,0,30 -chr6 52761898 rs2295605 T C 585.77 PASS AC=2;AF=1.0;AN=2;DB;DP=17;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.63;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.46;SOR=5.784;VQSLOD=7.27;culprit=FS;GENE=GSTA3 GT:AD:DP:GQ:PL 1/1:0,17:17:51:614,51,0 -chr6 52766192 rs6935603 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=GSTA3 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52767869 rs542113 T A 53.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=8.36;culprit=FS;GENE=GSTA3 GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 52768392 . CA C 63.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.806;ClippingRankSum=-0.832;DP=73;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.1;MQ0=0;MQRankSum=1.36;QD=0.87;ReadPosRankSum=-1.466;SOR=0.111;VQSLOD=2.98;culprit=FS;GENE=GSTA3 GT:AD:DP:GQ:PL 0/1:42,11:53:99:101,0,838 -chr6 52785560 rs689167 G A 446.77 PASS AC=2;AF=1.0;AN=2;DB;DP=13;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.37;SOR=0.836;VQSLOD=7.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,13:13:39:475,39,0 -chr6 52785580 rs689197 G A 546.77 PASS AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.55;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.17;SOR=0.693;VQSLOD=6.6;culprit=FS GT:AD:DP:GQ:PL 1/1:0,16:16:48:575,48,0 -chr6 52785649 rs581594 G A 388.77 PASS AC=2;AF=1.0;AN=2;DB;DP=11;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.47;SOR=4.804;VQSLOD=6.33;culprit=FS GT:AD:DP:GQ:PL 1/1:0,10:10:30:417,30,0 -chr6 52795274 rs547362 G T 47.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=0.693;VQSLOD=8.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 52802244 rs371403 A G 109.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.26;SOR=1.609;VQSLOD=7.67;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:137,12,0 -chr6 52820382 rs10948733 G A 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.62;culprit=FS;GENE=GSTA9P GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 52835606 rs571672 T C 114.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.51;SOR=3.258;VQSLOD=6.85;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:142,12,0 -chr6 52839185 rs428957 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52843131 rs367836 G T 2227.77 PASS AC=2;AF=1.0;AN=2;DB;DP=54;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.34;SOR=8.015;VQSLOD=7.12;culprit=FS;GENE=GSTA4 GT:AD:DP:GQ:PL 1/1:0,54:54:99:2256,163,0 -chr6 52843477 rs375887 A G 995.77 PASS AC=2;AF=1.0;AN=2;DB;DP=26;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.28;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.52;SOR=5.058;VQSLOD=6.33;culprit=FS;GENE=GSTA4,RNY3P15 GT:AD:DP:GQ:PL 1/1:0,25:25:75:1024,75,0 -chr6 52843524 rs543613 T C 344.78 PASS AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.54;SOR=4.615;VQSLOD=4.87;culprit=FS;GENE=GSTA4,RNY3P15 GT:AD:DP:GQ:PL 1/1:0,9:9:27:373,27,0 -chr6 52847150 rs67390777 TA T 38.25 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=66.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=12.75;SOR=2.833;VQSLOD=8.55;culprit=FS;GENE=GSTA4 GT:AD:DP:GQ:PL 1/1:0,3:3:9:75,9,0 -chr6 52847273 rs3831189 T TAC 756.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.167;ClippingRankSum=0.026;DB;DP=33;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=61.26;MQ0=0;MQRankSum=-0.078;POSITIVE_TRAIN_SITE;QD=22.93;ReadPosRankSum=0.544;SOR=2.621;VQSLOD=6.58;culprit=FS;GENE=GSTA4 GT:AD:DP:GQ:PL 0/1:6,24:30:99:794,0,101 -chr6 52847551 rs316133 G C 3193.77 PASS AC=2;AF=1.0;AN=2;DB;DP=83;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.72;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.28;SOR=2.833;VQSLOD=6.64;culprit=FS;GENE=GSTA4 GT:AD:DP:GQ:PL 1/1:0,83:83:99:3222,249,0 -chr6 52847682 rs10557482 GGAGA G 232.8 PASS AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=62.36;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=3.912;VQSLOD=6.22;culprit=FS;GENE=GSTA4 GT:AD:DP:GQ:PL 1/1:0,6:6:18:270,18,0 -chr6 52849146 rs316128 G T 959.77 PASS AC=2;AF=1.0;AN=2;DB;DP=28;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.28;SOR=5.136;VQSLOD=6.09;culprit=FS;GENE=GSTA4 GT:AD:DP:GQ:PL 1/1:0,26:26:78:988,78,0 -chr6 52849481 . C CT 353.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.178;ClippingRankSum=-1.73;DP=59;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.53;MQ0=0;MQRankSum=-0.663;POSITIVE_TRAIN_SITE;QD=6.0;ReadPosRankSum=-1.275;SOR=1.609;VQSLOD=5.78;culprit=FS;GENE=GSTA4 GT:AD:DP:GQ:PL 0/1:14,23:37:99:391,0,172 -chr6 52850040 rs669674 A G 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=8.43;culprit=FS;GENE=GSTA4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 52851936 rs508078 T C 1473.77 PASS AC=2;AF=1.0;AN=2;DB;DP=38;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.45;SOR=5.031;VQSLOD=7.06;culprit=FS;GENE=GSTA4 GT:AD:DP:GQ:PL 1/1:0,38:38:99:1502,114,0 -chr6 52881235 rs11756408 C T 143.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-0.198;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.198;POSITIVE_TRAIN_SITE;QD=20.54;ReadPosRankSum=-0.922;SOR=1.609;VQSLOD=5.81;culprit=FS;GENE=ICK GT:AD:DP:GQ:PL 0/1:2,5:7:63:172,0,63 -chr6 52892683 rs222456 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=ICK GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52929010 rs11401639 A AT 12.93 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=6.47;SOR=0.693;GENE=FBXO9 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52938468 . AT A 1342.73 PASS AC=2;AF=1.0;AN=2;BaseQRankSum=-0.585;ClippingRankSum=-0.022;DP=99;FS=6.337;MLEAC=2;MLEAF=1.0;MQ=60.68;MQ0=0;MQRankSum=-0.412;POSITIVE_TRAIN_SITE;QD=13.56;ReadPosRankSum=-1.299;SOR=3.952;VQSLOD=1.47;culprit=FS;GENE=FBXO9 GT:AD:DP:GQ:PL 1/1:2,62:64:99:1380,141,0 -chr6 52941597 rs34970749 TA T 32.71 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=16.35;SOR=0.693;VQSLOD=7.09;culprit=FS;GENE=FBXO9 GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 -chr6 52943841 rs35757290 TA T 559.73 PASS AC=2;AF=1.0;AN=2;DB;DP=18;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.53;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.1;SOR=5.67;VQSLOD=5.92;culprit=FS;GENE=FBXO9 GT:AD:DP:GQ:PL 1/1:0,16:16:48:597,48,0 -chr6 52958479 rs2816350 A G 1666.77 PASS AC=2;AF=1.0;AN=2;DB;DP=45;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.49;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.21;SOR=3.816;VQSLOD=6.04;culprit=FS;GENE=FBXO9 GT:AD:DP:GQ:PL 1/1:0,44:44:99:1695,132,0 -chr6 52962715 rs2744455 C T 1715.77 PASS AC=2;AF=1.0;AN=2;DB;DP=44;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.2;SOR=6.184;VQSLOD=5.9;culprit=FS;GENE=FBXO9 GT:AD:DP:GQ:PL 1/1:0,44:44:99:1744,132,0 -chr6 52985368 rs6919768 T G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52992851 rs377590473 AGAAGG A 35.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.663;ClippingRankSum=1.055;DB;DP=21;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.25;MQ0=0;MQRankSum=-2.362;QD=1.7;ReadPosRankSum=0.28;SOR=0.043;VQSLOD=3.98;culprit=FS;GENE=GCM1 GT:AD:DP:GQ:PL 0/1:18,3:21:73:73,0,1155 -chr6 52998788 rs2816346 G A 128.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.01;SOR=3.258;VQSLOD=7.97;culprit=FS;GENE=GCM1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:156,12,0 -chr6 52998834 rs2816345 C T 125.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.247;ClippingRankSum=-0.163;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.55;MQ0=0;MQRankSum=-0.054;POSITIVE_TRAIN_SITE;QD=7.86;ReadPosRankSum=1.464;SOR=0.307;VQSLOD=5.43;culprit=QD;GENE=GCM1 GT:AD:DP:GQ:PL 0/1:10,6:16:99:154,0,317 -chr6 52998856 rs2518573 T G 225.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.191;ClippingRankSum=0.439;DB;DP=25;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.13;MQ0=0;MQRankSum=-0.322;POSITIVE_TRAIN_SITE;QD=9.03;ReadPosRankSum=-0.966;SOR=0.412;VQSLOD=4.85;culprit=FS;GENE=GCM1 GT:AD:DP:GQ:PL 0/1:14,10:24:99:254,0,473 -chr6 53010182 rs9367511 A G 116.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.927;ClippingRankSum=-0.533;DB;DP=13;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.212;POSITIVE_TRAIN_SITE;QD=8.98;ReadPosRankSum=1.092;SOR=0.368;VQSLOD=5.93;culprit=FS;GENE=GCM1 GT:AD:DP:GQ:PL 0/1:8,5:13:99:145,0,291 -chr6 53010609 rs59049517 TA T 57.9 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.731;ClippingRankSum=0.731;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=61.53;MQ0=0;MQRankSum=-0.731;POSITIVE_TRAIN_SITE;QD=8.27;ReadPosRankSum=0.731;SOR=1.981;VQSLOD=6.42;culprit=FS;GENE=GCM1 GT:AD:DP:GQ:PL 0/1:1,4:5:14:95,0,14 -chr6 53061391 rs78303998 G A 114.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.017;ClippingRankSum=-0.421;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.922;QD=14.35;ReadPosRankSum=0.421;SOR=0.693;VQSLOD=4.6;culprit=FS;GENE=SOD1P1 GT:AD:DP:GQ:PL 0/1:4,4:8:99:143,0,121 -chr6 53062469 rs7772870 G A 98.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.76;SOR=1.179;VQSLOD=7.95;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:126,9,0 -chr6 53071745 rs77744774 C T 100.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.48;ClippingRankSum=-1.271;DB;DP=10;FS=6.99;MLEAC=1;MLEAF=0.5;MQ=41.67;MQ0=0;MQRankSum=-1.733;QD=10.08;ReadPosRankSum=0.0;SOR=4.407;VQSLOD=-0.7559;culprit=FS GT:AD:DP:GQ:PL 0/1:2,8:10:38:129,0,38 -chr6 53072388 rs62413047 A C 120.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.447;ClippingRankSum=-0.365;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.036;POSITIVE_TRAIN_SITE;QD=12.08;ReadPosRankSum=1.133;SOR=1.329;VQSLOD=4.69;culprit=FS GT:AD:DP:GQ:PL 0/1:4,6:10:99:149,0,125 -chr6 53072441 rs11758224 A G 29.77 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=1.067;ClippingRankSum=-1.067;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.572;QD=3.72;ReadPosRankSum=-1.067;SOR=0.693 GT:AD:DP:GQ:PL 0/1:6,2:8:58:58,0,221 -chr6 53072501 rs11756086 T C 22.79 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-1.495;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.198;QD=3.26;ReadPosRankSum=-0.198;SOR=1.802 GT:AD:DP:GQ:PL 0/1:5,2:7:51:51,0,184 -chr6 53103062 rs10583094 TAC T 36.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.35;SOR=0.693;VQSLOD=8.72;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 -chr6 53119938 . G T 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 -chr6 53120011 . C T 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53173704 rs209484 C T 29.79 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=9.93;ReadPosRankSum=-0.736;SOR=0.223;GENE=ELOVL5 GT:AD:DP:GQ:PL 0/1:1,2:3:25:58,0,25 -chr6 53186203 rs209499 C T 50.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=2.303;VQSLOD=8.79;culprit=FS;GENE=ELOVL5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 53210951 rs209523 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=ELOVL5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53229240 rs1346602 C T 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=7.63;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 53302223 rs11967914 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53306308 rs1401156 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53325093 rs11969450 G A 33.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=11.26;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=5.93;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:34:62,0,34 -chr6 53363487 rs10604357 GGGCT G 931.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.719;ClippingRankSum=0.942;DB;DP=65;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.9;MQ0=0;MQRankSum=-0.356;POSITIVE_TRAIN_SITE;QD=14.33;ReadPosRankSum=0.364;SOR=1.141;VQSLOD=6.29;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 0/1:37,26:63:99:969,0,1920 -chr6 53365019 rs661346 G C 4389.77 PASS AC=2;AF=1.0;AN=2;DB;DP=126;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.49;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.84;SOR=1.262;VQSLOD=6.97;culprit=QD;GENE=GCLC GT:AD:DP:GQ:PL 1/1:0,125:125:99:4418,375,0 -chr6 53366008 rs12525473 C T 48.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.18;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 53366061 rs12525474 C T 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=9.08;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 53370107 rs661603 T C 253.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.678;ClippingRankSum=0.998;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.103;POSITIVE_TRAIN_SITE;QD=15.86;ReadPosRankSum=-0.578;SOR=0.693;VQSLOD=6.35;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 0/1:8,8:16:99:282,0,260 -chr6 53370327 rs17884019 C T 446.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.961;ClippingRankSum=-0.471;DB;DP=32;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.3;POSITIVE_TRAIN_SITE;QD=13.96;ReadPosRankSum=0.848;SOR=1.112;VQSLOD=4.7;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 0/1:16,16:32:99:475,0,461 -chr6 53372145 rs1555903 T C 760.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=5.717;ClippingRankSum=-1.83;DB;DP=57;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.171;POSITIVE_TRAIN_SITE;QD=13.35;ReadPosRankSum=0.024;SOR=0.385;VQSLOD=5.78;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 0/1:34,23:57:99:789,0,1142 -chr6 53373197 rs2235707 G C 375.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.581;ClippingRankSum=-1.193;DB;DP=25;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.25;POSITIVE_TRAIN_SITE;QD=15.03;ReadPosRankSum=0.028;SOR=0.387;VQSLOD=5.68;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 0/1:15,10:25:99:404,0,860 -chr6 53373198 rs17880319 A G 375.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.38;ClippingRankSum=-0.765;DB;DP=27;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.913;POSITIVE_TRAIN_SITE;QD=13.92;ReadPosRankSum=0.716;SOR=0.404;VQSLOD=4.81;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 0/1:16,11:27:99:404,0,860 -chr6 53373276 rs17881410 C T 1348.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.532;ClippingRankSum=-1.183;DB;DP=82;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.72;MQ0=0;MQRankSum=0.107;POSITIVE_TRAIN_SITE;QD=16.45;ReadPosRankSum=0.654;SOR=0.742;VQSLOD=4.98;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 0/1:40,42:82:99:1377,0,1369 -chr6 53373624 rs3830795 G GCTCCAC 706.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.129;ClippingRankSum=-1.149;DB;DP=50;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=50.77;MQ0=0;MQRankSum=-5.319;POSITIVE_TRAIN_SITE;QD=14.13;ReadPosRankSum=-0.966;SOR=0.399;VQSLOD=1.11;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 0/1:29,20:49:99:744,0,1894 -chr6 53378861 rs11385177 A AT 433.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.124;ClippingRankSum=-1.535;DB;DP=30;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.249;POSITIVE_TRAIN_SITE;QD=14.46;ReadPosRankSum=0.456;SOR=0.693;VQSLOD=6.6;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 0/1:15,15:30:99:471,0,469 -chr6 53379193 rs17885705 A T 3122.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.101;ClippingRankSum=-0.402;DB;DP=206;FS=0.54;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.173;POSITIVE_TRAIN_SITE;QD=15.16;ReadPosRankSum=1.72;SOR=0.781;VQSLOD=1.97;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 0/1:103,103:206:99:3151,0,3088 -chr6 53379352 rs17881444 A G 1554.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.383;ClippingRankSum=1.328;DB;DP=104;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.133;POSITIVE_TRAIN_SITE;QD=14.95;ReadPosRankSum=1.368;SOR=0.719;VQSLOD=3.93;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 0/1:55,49:104:99:1583,0,1676 -chr6 53379405 rs3736729 A C 1019.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.536;ClippingRankSum=0.059;DB;DP=50;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.059;POSITIVE_TRAIN_SITE;QD=20.4;ReadPosRankSum=-1.69;SOR=1.051;VQSLOD=4.96;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 0/1:21,29:50:99:1048,0,693 -chr6 53379499 rs17883806 G C 182.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.133;ClippingRankSum=-2.383;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.866;POSITIVE_TRAIN_SITE;QD=18.28;ReadPosRankSum=-0.741;SOR=1.085;VQSLOD=5.36;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 0/1:4,6:10:99:211,0,139 -chr6 53385934 rs17883816 T C 291.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.062;ClippingRankSum=0.766;DB;DP=15;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.237;POSITIVE_TRAIN_SITE;QD=19.45;ReadPosRankSum=1.591;SOR=1.112;VQSLOD=4.79;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 0/1:6,9:15:99:320,0,184 -chr6 53394065 rs17883125 C T 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=7.91;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 53409451 . C CCCT 53.7 PASS AC=2;AF=1.0;AN=2;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;QD=13.43;SOR=2.303;VQSLOD=6.3;culprit=FS;GENE=GCLC GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 53470507 rs9349679 G A 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=GCLC GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 -chr6 53493640 rs6925537 T C 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.13;SOR=1.609;VQSLOD=6.84;culprit=FS;GENE=LINC01564 GT:AD:DP:GQ:PL 1/1:0,1:1:6:83,6,0 -chr6 53493642 rs6903184 G C 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=7.55;culprit=FS;GENE=LINC01564 GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 53516876 rs6928338 T G 250.78 PASS AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=38.13;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.86;SOR=0.892;VQSLOD=6.06;culprit=FS;GENE=KLHL31 GT:AD:DP:GQ:PL 1/1:0,9:9:27:279,27,0 -chr6 53519062 rs10948758 A G 5150.77 PASS AC=2;AF=1.0;AN=2;DB;DP=125;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.82;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.87;SOR=0.882;VQSLOD=6.17;culprit=FS;GENE=KLHL31 GT:AD:DP:GQ:PL 1/1:0,125:125:99:5179,376,0 -chr6 53519605 rs3799260 C T 7091.77 PASS AC=2;AF=1.0;AN=2;DB;DP=190;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.76;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.12;SOR=0.693;VQSLOD=2.98;culprit=FS;GENE=KLHL31 GT:AD:DP:GQ:PL 1/1:0,190:190:99:7120,571,0 -chr6 53519857 rs12210809 G A 4207.77 PASS AC=2;AF=1.0;AN=2;DB;DP=112;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.55;MQ0=0;POSITIVE_TRAIN_SITE;QD=36.51;SOR=1.22;VQSLOD=5.94;culprit=QD;GENE=KLHL31 GT:AD:DP:GQ:PL 1/1:0,110:110:99:4236,331,0 -chr6 53520088 rs2038939 T C 2813.77 PASS AC=2;AF=1.0;AN=2;DB;DP=69;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.28;SOR=3.643;VQSLOD=5.42;culprit=FS;GENE=KLHL31 GT:AD:DP:GQ:PL 1/1:0,69:69:99:2842,207,0 -chr6 53520124 rs2038940 A G 1799.77 PASS AC=2;AF=1.0;AN=2;DB;DP=46;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.5;MQ0=0;QD=29.97;SOR=6.273;VQSLOD=4.73;culprit=FS;GENE=KLHL31 GT:AD:DP:GQ:PL 1/1:0,46:46:99:1828,138,0 -chr6 53528784 rs1326553 A G 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.43;culprit=FS;GENE=KLHL31 GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 53529027 rs1326554 A T 3242.77 PASS AC=2;AF=1.0;AN=2;DB;DP=87;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=37.3;SOR=4.929;VQSLOD=5.98;culprit=QD;GENE=KLHL31 GT:AD:DP:GQ:PL 1/1:0,87:87:99:3271,262,0 -chr6 53543213 rs4541744 C T 99.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.09;SOR=1.179;VQSLOD=7.91;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:127,9,0 -chr6 53559094 rs10452610 A G 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.57;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 53586617 rs35610624 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53601883 rs7745277 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53606394 rs4457161 T C 12.07 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:23:40,0,23 -chr6 53620789 rs7763482 C T 53.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=2.303;VQSLOD=9.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 53626319 . G C 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53654033 rs3001010 C T 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.63;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 53662935 rs9382237 C T 53.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=6.56;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 53674284 rs4475321 C T 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=7.61;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 53676354 rs4715425 G A 91.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=1.179;VQSLOD=7.98;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:119,9,0 -chr6 53690779 rs3003489 T C 46.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.37;SOR=2.303;VQSLOD=8.83;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:74,6,0 -chr6 53691835 rs7755924 A G 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.14;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 53694407 rs6904545 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=LRRC1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53707098 rs4286781 C T 4179.77 PASS AC=2;AF=1.0;AN=2;DB;DP=110;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.61;SOR=2.876;VQSLOD=6.95;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 1/1:0,110:110:99:4208,331,0 -chr6 53723062 rs145334901 AT A 13.89 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=6.94;SOR=2.303;GENE=LRRC1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:50,6,0 -chr6 53726761 rs3935663 C T 47.79 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=15.93;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.71;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 0/1:1,2:3:22:76,0,22 -chr6 53726780 rs3935664 A G 90.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.09;SOR=1.179;VQSLOD=9.22;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:118,9,0 -chr6 53749074 rs4265034 G C 79.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.43;SOR=2.833;VQSLOD=8.11;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:107,9,0 -chr6 53755300 rs6458972 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=LRRC1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53762210 rs62397108 C A 270.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.681;ClippingRankSum=-0.033;DB;DP=23;FS=4.904;MLEAC=1;MLEAF=0.5;MQ=59.19;MQ0=0;MQRankSum=0.824;POSITIVE_TRAIN_SITE;QD=11.77;ReadPosRankSum=0.89;SOR=2.165;VQSLOD=2.61;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 0/1:12,10:22:99:299,0,376 -chr6 53764829 rs71558840 T G 125.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.804;ClippingRankSum=1.304;DB;DP=26;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=39.8;MQ0=0;MQRankSum=2.136;QD=4.84;ReadPosRankSum=1.969;SOR=0.387;VQSLOD=1.71;culprit=QD;GENE=LRRC1 GT:AD:DP:GQ:PL 0/1:15,10:25:99:154,0,298 -chr6 53778661 rs201915048 T G 38.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-5.938;ClippingRankSum=-0.459;DB;DP=84;FS=136.465;MLEAC=1;MLEAF=0.5;MQ=49.9;MQ0=0;MQRankSum=-5.277;QD=0.46;ReadPosRankSum=-6.784;SOR=6.271;VQSLOD=-42.91;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 0/1:61,22:83:67:67,0,1974 -chr6 53784268 rs59246960 C CT 332.73 PASS AC=2;AF=1.0;AN=2;DB;DP=17;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=54.32;MQ0=0;QD=19.57;SOR=5.549;VQSLOD=4.44;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 1/1:0,15:15:45:370,45,0 -chr6 53784662 rs3777661 A G 109.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.922;ClippingRankSum=0.0;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.421;POSITIVE_TRAIN_SITE;QD=13.72;ReadPosRankSum=-0.421;SOR=0.693;VQSLOD=6.47;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 0/1:4,4:8:99:138,0,134 -chr6 53785276 rs2294789 C A 178.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.383;ClippingRankSum=-0.365;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.365;POSITIVE_TRAIN_SITE;QD=17.88;ReadPosRankSum=-2.072;SOR=1.085;VQSLOD=5.18;culprit=ReadPosRankSum;GENE=LRRC1 GT:AD:DP:GQ:PL 0/1:4,6:10:99:207,0,141 -chr6 53785759 rs201940946 G GT 45.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.55;ClippingRankSum=-0.55;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=61.34;MQ0=0;MQRankSum=-0.55;QD=5.72;ReadPosRankSum=-0.937;SOR=0.941;VQSLOD=4.79;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 0/1:3,4:7:54:83,0,54 -chr6 53787267 rs2294791 G C 221.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.074;ClippingRankSum=1.656;DB;DP=13;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.935;POSITIVE_TRAIN_SITE;QD=17.06;ReadPosRankSum=0.101;SOR=0.836;VQSLOD=6.75;culprit=FS;GENE=LRRC1 GT:AD:DP:GQ:PL 0/1:6,7:13:99:250,0,220 -chr6 53805460 rs6907354 A G 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.61;culprit=FS;GENE=MLIP GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 53893735 . C A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=MLIP GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53927326 rs4715439 T C 62.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.26;culprit=FS;GENE=MLIP GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 53953083 . A G 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=MLIP GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53973251 . G T 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=MLIP GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53982990 rs4521576 A C 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.14;culprit=FS;GENE=MLIP GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 53986503 rs2145754 A T 180.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.749;ClippingRankSum=1.186;DB;DP=11;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.466;POSITIVE_TRAIN_SITE;QD=16.43;ReadPosRankSum=1.932;SOR=0.859;VQSLOD=6.2;culprit=FS;GENE=MLIP GT:AD:DP:GQ:PL 0/1:5,6:11:99:209,0,162 -chr6 53989526 rs4712056 G A 2189.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.153;ClippingRankSum=1.695;DB;DP=131;FS=6.808;MLEAC=1;MLEAF=0.5;MQ=59.82;MQ0=0;MQRankSum=-1.076;POSITIVE_TRAIN_SITE;QD=16.72;ReadPosRankSum=1.657;SOR=0.326;VQSLOD=1.81;culprit=FS;GENE=MLIP GT:AD:DP:GQ:PL 0/1:59,70:129:99:2218,0,1820 -chr6 54003899 rs11965480 A G 59.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=8.24;culprit=FS;GENE=MLIP GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 54013765 rs2145755 A G 923.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.107;ClippingRankSum=0.838;DB;DP=48;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.142;POSITIVE_TRAIN_SITE;QD=19.25;ReadPosRankSum=0.735;SOR=0.866;VQSLOD=4.39;culprit=FS;GENE=MLIP GT:AD:DP:GQ:PL 0/1:22,26:48:99:952,0,728 -chr6 54025155 rs10484648 T C 760.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.724;ClippingRankSum=0.655;DB;DP=56;FS=1.455;MLEAC=1;MLEAF=0.5;MQ=59.59;MQ0=0;MQRankSum=-0.099;POSITIVE_TRAIN_SITE;QD=13.59;ReadPosRankSum=0.458;SOR=1.151;VQSLOD=3.37;culprit=FS;GENE=MLIP GT:AD:DP:GQ:PL 0/1:30,23:53:99:789,0,990 -chr6 54030072 rs1280860 T C 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.53;culprit=FS;GENE=MLIP GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 54035531 rs2792626 T C 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=9.15;culprit=FS;GENE=MLIP GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 54046086 rs2792632 A C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=MLIP GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54054686 rs6934690 T A 2471.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.306;ClippingRankSum=-2.348;DB;DP=167;FS=1.953;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.357;POSITIVE_TRAIN_SITE;QD=14.8;ReadPosRankSum=1.55;SOR=0.892;VQSLOD=2.86;culprit=DP;GENE=MLIP GT:AD:DP:GQ:PL 0/1:79,88:167:99:2500,0,2110 -chr6 54054837 rs9296739 A G 811.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.037;ClippingRankSum=-2.468;DB;DP=45;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.876;POSITIVE_TRAIN_SITE;QD=18.04;ReadPosRankSum=-1.149;SOR=0.829;VQSLOD=5.35;culprit=FS;GENE=MLIP GT:AD:DP:GQ:PL 0/1:21,24:45:99:840,0,675 -chr6 54058426 . G T 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=MLIP GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54067088 rs67016420 AT A 245.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.88;ClippingRankSum=-0.81;DB;DP=24;FS=3.222;MLEAC=1;MLEAF=0.5;MQ=62.65;MQ0=0;MQRankSum=1.303;POSITIVE_TRAIN_SITE;QD=10.24;ReadPosRankSum=0.88;SOR=0.16;VQSLOD=2.56;culprit=MQRankSum;GENE=MLIP GT:AD:DP:GQ:PL 0/1:11,10:21:99:283,0,313 -chr6 54095411 rs2275770 C G 1855.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.478;ClippingRankSum=-0.434;DB;DP=111;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.74;MQ0=0;MQRankSum=1.03;POSITIVE_TRAIN_SITE;QD=16.72;ReadPosRankSum=-1.101;SOR=0.609;VQSLOD=4.2;culprit=FS;GENE=MLIP GT:AD:DP:GQ:PL 0/1:58,53:111:99:1884,0,2350 -chr6 54095423 rs816384 T C 2503.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=6.058;ClippingRankSum=-0.087;DB;DP=130;FS=7.052;MLEAC=1;MLEAF=0.5;MQ=58.75;MQ0=0;MQRankSum=-0.073;POSITIVE_TRAIN_SITE;QD=19.26;ReadPosRankSum=0.105;SOR=2.758;VQSLOD=0.745;culprit=FS;GENE=MLIP GT:AD:DP:GQ:PL 0/1:58,72:130:99:2532,0,2153 -chr6 54095524 rs2275769 C T 4212.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.148;ClippingRankSum=1.384;DB;DP=307;FS=2.75;MLEAC=1;MLEAF=0.5;MQ=59.09;MQ0=0;MQRankSum=-1.33;POSITIVE_TRAIN_SITE;QD=13.72;ReadPosRankSum=0.874;SOR=0.887;VQSLOD=1.41;culprit=DP;GENE=MLIP GT:AD:DP:GQ:PL 0/1:165,138:303:99:4241,0,5117 -chr6 54157748 rs6458990 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54157803 rs149997923 G GTT 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=7.05;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 54157804 rs13211037 A T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.75;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 54159866 rs7775058 C T 83.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.76;SOR=1.179;VQSLOD=7.56;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:111,9,0 -chr6 54159915 rs7740868 G T 64.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=2.833;VQSLOD=8.16;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:92,9,0 -chr6 54166206 . T C 62.74 PASS AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 54166208 . CA C 43.79 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=14.6;SOR=0.223;VQSLOD=4.47;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:19:81,0,19 -chr6 54173085 rs2297981 T A 239.8 PASS AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.26;SOR=4.174;VQSLOD=7.06;culprit=FS;GENE=TINAG GT:AD:DP:GQ:PL 1/1:0,7:7:21:268,21,0 -chr6 54175705 rs148816365 C CTTTCTT 143 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=34.37;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.01;SOR=1.609;VQSLOD=8.24;culprit=FS;GENE=TINAG GT:AD:DP:GQ:PL 1/1:0,4:4:12:180,12,0 -chr6 54185689 rs2297983 G T 92.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.44;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.76;SOR=2.833;VQSLOD=9.04;culprit=FS;GENE=TINAG GT:AD:DP:GQ:PL 1/1:0,3:3:9:120,9,0 -chr6 54186024 rs2297986 T C 1611.77 PASS AC=2;AF=1.0;AN=2;DB;DP=43;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.67;SOR=5.235;VQSLOD=7.3;culprit=FS;GENE=TINAG GT:AD:DP:GQ:PL 1/1:0,42:42:99:1640,126,0 -chr6 54186147 rs1058768 T C 3340.77 PASS AC=2;AF=1.0;AN=2;DB;DP=91;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.94;SOR=0.906;VQSLOD=4.55;culprit=FS;GENE=TINAG GT:AD:DP:GQ:PL 1/1:0,91:91:99:3369,274,0 -chr6 54191363 rs9370289 G A 180.9 PASS AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.88;SOR=3.611;VQSLOD=5.85;culprit=FS;GENE=TINAG GT:AD:DP:GQ:PL 1/1:0,5:5:15:209,15,0 -chr6 54191970 rs1848440 T A 4352.77 PASS AC=2;AF=1.0;AN=2;DB;DP=121;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.31;SOR=3.556;VQSLOD=5.9;culprit=FS;GENE=TINAG GT:AD:DP:GQ:PL 1/1:0,121:121:99:4381,364,0 -chr6 54208353 rs1417387 T C 185.84 PASS AC=2;AF=1.0;AN=2;DB;DP=6;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.97;SOR=3.912;VQSLOD=6.78;culprit=FS;GENE=TINAG GT:AD:DP:GQ:PL 1/1:0,6:6:18:214,18,0 -chr6 54212964 rs1876606 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=TINAG GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54349833 rs2294725 G A 95.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.017;ClippingRankSum=0.0;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=43.31;MQ0=0;MQRankSum=0.421;POSITIVE_TRAIN_SITE;QD=11.97;ReadPosRankSum=-1.368;SOR=0.693;VQSLOD=5.69;culprit=FS;GENE=CLNS1AP1 GT:AD:DP:GQ:PL 0/1:4,4:8:99:124,0,121 -chr6 54350048 rs807991 G A 997.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.754;ClippingRankSum=0.019;DB;DP=73;FS=12.208;MLEAC=1;MLEAF=0.5;MQ=57.55;MQ0=0;MQRankSum=1.161;POSITIVE_TRAIN_SITE;QD=13.67;ReadPosRankSum=0.551;SOR=0.108;VQSLOD=1.6;culprit=FS;GENE=CLNS1AP1 GT:AD:DP:GQ:PL 0/1:28,38:66:99:1026,0,963 -chr6 54350422 rs565623 G A 1056.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.722;ClippingRankSum=-0.634;DB;DP=67;FS=3.327;MLEAC=1;MLEAF=0.5;MQ=59.66;MQ0=0;MQRankSum=0.433;POSITIVE_TRAIN_SITE;QD=15.77;ReadPosRankSum=-1.01;SOR=1.142;VQSLOD=2.92;culprit=ReadPosRankSum;GENE=CLNS1AP1 GT:AD:DP:GQ:PL 0/1:32,35:67:99:1085,0,982 -chr6 54356832 rs3900305 T A 31.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=-1.231;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=6.35;ReadPosRankSum=0.358;SOR=0.368;VQSLOD=5.26;culprit=QD GT:AD:DP:GQ:PL 0/1:3,2:5:60:60,0,75 -chr6 54438922 rs10447409 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54467267 rs1951694 A G 44.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.92;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.23;culprit=FS;GENE=RPL10P10 GT:AD:DP:GQ:PL 0/1:1,2:3:32:73,0,32 -chr6 54477874 rs5876389 T TA 16.8 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=8.4;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:53,6,0 -chr6 54485844 rs7766941 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54489986 rs10948830 G A 2797.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-2.226;ClippingRankSum=-0.973;DB;DP=129;FS=4.335;MLEAC=1;MLEAF=0.5;MQ=59.28;MQ0=0;MQRankSum=1.3;NEGATIVE_TRAIN_SITE;QD=21.69;ReadPosRankSum=1.119;SOR=0.983;VQSLOD=-1.343;culprit=DP;GENE=RPSAP44 GT:AD:DP:GQ:PL 0/1:54,73:127:99:2826,0,2602 -chr6 54489990 rs10948831 A G 2774.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.682;ClippingRankSum=-0.704;DB;DP=125;FS=2.332;MLEAC=1;MLEAF=0.5;MQ=59.26;MQ0=0;MQRankSum=0.479;POSITIVE_TRAIN_SITE;QD=22.2;ReadPosRankSum=0.468;SOR=0.927;VQSLOD=0.604;culprit=DP;GENE=RPSAP44 GT:AD:DP:GQ:PL 0/1:52,71:123:99:2803,0,2545 -chr6 54490041 rs9349726 T C 2720.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=5.83;ClippingRankSum=-0.591;DB;DP=155;FS=2.034;MLEAC=1;MLEAF=0.5;MQ=58.04;MQ0=0;MQRankSum=2.054;POSITIVE_TRAIN_SITE;QD=17.55;ReadPosRankSum=0.525;SOR=0.513;VQSLOD=1.47;culprit=MQRankSum;GENE=RPSAP44 GT:AD:DP:GQ:PL 0/1:71,82:153:99:2749,0,2148 -chr6 54490338 rs10807475 T A 832.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.069;ClippingRankSum=-0.537;DB;DP=81;FS=11.744;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.204;POSITIVE_TRAIN_SITE;QD=10.28;ReadPosRankSum=0.105;SOR=0.051;VQSLOD=0.328;culprit=FS;GENE=RPSAP44 GT:AD:DP:GQ:PL 0/1:36,38:74:99:870,0,1117 -chr6 54500405 . A G 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54557514 rs1395632 G A 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:35:40,0,35 -chr6 54571089 rs6907631 T G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54635275 rs2397171 G C 38.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.72;ClippingRankSum=-0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.72;POSITIVE_TRAIN_SITE;QD=6.46;ReadPosRankSum=0.72;SOR=0.307;VQSLOD=5.95;culprit=QD;GENE=KRASP1 GT:AD:DP:GQ:PL 0/1:4,2:6:67:67,0,148 -chr6 54635398 rs5876400 T TG 256.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.6;ClippingRankSum=-2.0;DB;DP=14;FS=2.363;MLEAC=1;MLEAF=0.5;MQ=51.87;MQ0=0;MQRankSum=-1.733;POSITIVE_TRAIN_SITE;QD=18.34;ReadPosRankSum=-1.467;SOR=1.288;VQSLOD=1.73;culprit=MQRankSum;GENE=KRASP1 GT:AD:DP:GQ:PL 0/1:5,9:14:99:294,0,145 -chr6 54635417 rs4516942 G A 237.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.532;ClippingRankSum=-0.794;DB;DP=20;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.69;MQ0=0;MQRankSum=-1.172;POSITIVE_TRAIN_SITE;QD=11.89;ReadPosRankSum=-0.189;SOR=0.693;VQSLOD=4.98;culprit=FS;GENE=KRASP1 GT:AD:DP:GQ:PL 0/1:10,10:20:99:266,0,354 -chr6 54635605 rs73742825 C G 103.03 PASS AC=2;AF=1.0;AN=2;DB;DP=6;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=36.07;MQ0=0;QD=17.17;SOR=1.609;VQSLOD=3.97;culprit=FS;GENE=KRASP1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:131,12,0 -chr6 54661634 rs12216186 A G 59.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.16;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 54672835 rs10807480 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54682692 . C G 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54691959 . C A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54692294 rs72957572 A G 62.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.44;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 54734941 rs7765721 C A 557.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.038;ClippingRankSum=-1.807;DB;DP=46;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.5;MQ0=0;MQRankSum=0.312;POSITIVE_TRAIN_SITE;QD=12.13;ReadPosRankSum=0.089;SOR=0.412;VQSLOD=4.55;culprit=FS;GENE=FAM83B GT:AD:DP:GQ:PL 0/1:27,19:46:99:586,0,962 -chr6 54735122 rs1472679 A G 2623.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.37;ClippingRankSum=-0.594;DB;DP=179;FS=1.203;MLEAC=1;MLEAF=0.5;MQ=59.51;MQ0=0;MQRankSum=-0.157;POSITIVE_TRAIN_SITE;QD=14.66;ReadPosRankSum=1.205;SOR=0.798;VQSLOD=2.83;culprit=DP;GENE=FAM83B GT:AD:DP:GQ:PL 0/1:91,86:177:99:2652,0,2889 -chr6 54735594 rs995851 G A 418.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.928;ClippingRankSum=0.395;DB;DP=30;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.187;POSITIVE_TRAIN_SITE;QD=13.96;ReadPosRankSum=-0.686;SOR=0.576;VQSLOD=5.25;culprit=ReadPosRankSum;GENE=FAM83B GT:AD:DP:GQ:PL 0/1:16,14:30:99:447,0,581 -chr6 54735606 rs995852 G A 893.77 PASS AC=2;AF=1.0;AN=2;DB;DP=23;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.18;SOR=6.358;VQSLOD=6.01;culprit=FS;GENE=FAM83B GT:AD:DP:GQ:PL 1/1:0,23:23:69:922,69,0 -chr6 54792553 . G A 1230.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.237;ClippingRankSum=1.275;DP=82;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=36.68;MQ0=0;MQRankSum=-1.187;QD=15.01;ReadPosRankSum=-0.624;SOR=1.402;VQSLOD=3.32;culprit=FS;GENE=FAM83B GT:AD:DP:GQ:PL 0/1:27,48:75:99:1259,0,685 -chr6 54807006 rs171224 T G 114.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.638;ClippingRankSum=1.368;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.421;POSITIVE_TRAIN_SITE;QD=14.35;ReadPosRankSum=-0.421;SOR=0.693;VQSLOD=6.54;culprit=FS;GENE=FAM83B GT:AD:DP:GQ:PL 0/1:4,4:8:99:143,0,127 -chr6 54824610 . C A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54857680 rs2134536 G A 45.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.988;ClippingRankSum=0.406;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.406;POSITIVE_TRAIN_SITE;QD=7.63;ReadPosRankSum=0.988;SOR=0.693;VQSLOD=5.75;culprit=QD GT:AD:DP:GQ:PL 0/1:3,3:6:73:74,0,73 -chr6 54936685 rs57552002 T TAATA 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=7.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 54938529 rs4312988 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54998074 rs9370385 A G 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.03;culprit=FS;GENE=HCRTR2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 55003132 rs9349759 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=HCRTR2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55028053 rs200898132 CAACA C 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=50.6;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=6.89;culprit=FS;GENE=HCRTR2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 55028113 rs6459069 C T 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=50.6;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=9.01;culprit=FS;GENE=HCRTR2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 55040774 rs4615392 A G 50.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=0.693;VQSLOD=8.67;culprit=FS;GENE=HCRTR2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 55045025 rs9370399 A C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=HCRTR2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55113411 rs3122169 C A 2001.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.942;ClippingRankSum=-1.093;DB;DP=131;FS=4.929;MLEAC=1;MLEAF=0.5;MQ=59.47;MQ0=0;MQRankSum=-0.196;POSITIVE_TRAIN_SITE;QD=15.28;ReadPosRankSum=-0.937;SOR=1.302;VQSLOD=2.09;culprit=DP;GENE=HCRTR2 GT:AD:DP:GQ:PL 0/1:65,66:131:99:2030,0,2129 -chr6 55142337 rs2653349 A G 920.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.329;ClippingRankSum=-0.235;DB;DP=82;FS=3.142;MLEAC=1;MLEAF=0.5;MQ=57.13;MQ0=0;MQRankSum=0.602;POSITIVE_TRAIN_SITE;QD=11.23;ReadPosRankSum=1.94;SOR=1.11;VQSLOD=2.51;culprit=ReadPosRankSum;GENE=HCRTR2 GT:AD:DP:GQ:PL 0/1:47,31:78:99:949,0,1545 -chr6 55142458 rs11455646 C CT 65.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.309;ClippingRankSum=-1.788;DB;DP=22;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.78;MQ0=0;MQRankSum=0.244;POSITIVE_TRAIN_SITE;QD=2.99;ReadPosRankSum=-0.38;SOR=0.446;VQSLOD=6.64;culprit=FS;GENE=HCRTR2 GT:AD:DP:GQ:PL 0/1:7,7:14:99:103,0,107 -chr6 55190480 rs12110721 G A 59.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.76;SOR=1.179;VQSLOD=7.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:87,9,0 -chr6 55196299 rs4715531 C A 87.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.09;SOR=2.833;VQSLOD=9.04;culprit=FS;GENE=GFRAL GT:AD:DP:GQ:PL 1/1:0,3:3:9:115,9,0 -chr6 55196587 rs12199003 C T 2169.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.778;ClippingRankSum=1.972;DB;DP=139;FS=4.029;MLEAC=1;MLEAF=0.5;MQ=59.87;MQ0=0;MQRankSum=-0.737;POSITIVE_TRAIN_SITE;QD=15.61;ReadPosRankSum=1.585;SOR=0.438;VQSLOD=2.24;culprit=DP;GENE=GFRAL GT:AD:DP:GQ:PL 0/1:67,71:138:99:2198,0,1867 -chr6 55206112 rs7761953 G C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=GFRAL GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55215079 rs1032767 G A 1033.77 PASS AC=2;AF=1.0;AN=2;DB;DP=27;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.33;SOR=5.211;VQSLOD=6.59;culprit=FS;GENE=GFRAL GT:AD:DP:GQ:PL 1/1:0,27:27:81:1062,81,0 -chr6 55215155 rs7743512 C T 247.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.106;ClippingRankSum=1.059;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.106;POSITIVE_TRAIN_SITE;QD=15.49;ReadPosRankSum=-1.164;SOR=0.976;VQSLOD=5.41;culprit=FS;GENE=GFRAL GT:AD:DP:GQ:PL 0/1:7,9:16:99:276,0,215 -chr6 55216005 rs870806 G A 1207.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.265;ClippingRankSum=0.451;DB;DP=75;FS=2.105;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.005;POSITIVE_TRAIN_SITE;QD=16.1;ReadPosRankSum=0.589;SOR=0.234;VQSLOD=3.38;culprit=DP;GENE=GFRAL GT:AD:DP:GQ:PL 0/1:36,39:75:99:1236,0,1296 -chr6 55223501 rs41474045 T G 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=9.2;culprit=FS;GENE=GFRAL GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 55223531 rs62419074 A G 95.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.763;ClippingRankSum=1.11;DB;DP=15;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.457;POSITIVE_TRAIN_SITE;QD=6.38;ReadPosRankSum=0.457;SOR=0.16;VQSLOD=4.75;culprit=QD;GENE=GFRAL GT:AD:DP:GQ:PL 0/1:11,4:15:99:124,0,384 -chr6 55223962 . G GTCTATCTATCTATCTA 839.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.176;ClippingRankSum=1.806;DP=80;FS=1.944;MLEAC=1;MLEAF=0.5;MQ=57.42;MQ0=0;MQRankSum=-1.121;POSITIVE_TRAIN_SITE;QD=10.5;ReadPosRankSum=-2.584;SOR=0.237;VQSLOD=1.23;culprit=ReadPosRankSum;GENE=GFRAL GT:AD:DP:GQ:PL 0/1:30,22:52:99:877,0,3184 -chr6 55224107 rs9475257 A G 80.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.231;POSITIVE_TRAIN_SITE;QD=16.15;ReadPosRankSum=1.231;SOR=1.022;VQSLOD=5.3;culprit=FS;GENE=GFRAL GT:AD:DP:GQ:PL 0/1:2,3:5:65:109,0,65 -chr6 55227565 rs17830060 T C 48.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.57;culprit=FS;GENE=GFRAL GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 55227593 rs9475263 C T 30.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.72;ClippingRankSum=0.0;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.04;MQ0=0;MQRankSum=1.38;POSITIVE_TRAIN_SITE;QD=5.13;ReadPosRankSum=-0.72;SOR=1.179;VQSLOD=5.45;culprit=QD;GENE=GFRAL GT:AD:DP:GQ:PL 0/1:4,2:6:59:59,0,110 -chr6 55227683 rs9475264 C G 70.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.248;ClippingRankSum=-0.248;DB;DP=9;FS=3.01;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.573;POSITIVE_TRAIN_SITE;QD=7.86;ReadPosRankSum=1.203;SOR=1.911;VQSLOD=1.76;culprit=QD;GENE=GFRAL GT:AD:DP:GQ:PL 0/1:6,3:9:99:99,0,193 -chr6 55227930 rs35444148 CA C 43.25 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=14.42;SOR=2.833;VQSLOD=8.08;culprit=FS;GENE=GFRAL GT:AD:DP:GQ:PL 1/1:0,3:3:9:80,9,0 -chr6 55258643 rs28479599 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=GFRAL GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55263789 rs9396088 C T 128.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.01;SOR=3.258;VQSLOD=7.51;culprit=FS;GENE=GFRAL GT:AD:DP:GQ:PL 1/1:0,4:4:12:156,12,0 -chr6 55263921 rs41271314 T C 376.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.406;ClippingRankSum=0.798;DB;DP=32;FS=4.26;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.044;POSITIVE_TRAIN_SITE;QD=11.77;ReadPosRankSum=0.136;SOR=0.078;VQSLOD=2.13;culprit=MQRankSum;GENE=GFRAL GT:AD:DP:GQ:PL 0/1:20,12:32:99:405,0,694 -chr6 55264362 rs6936510 T C 1182.77 PASS AC=2;AF=1.0;AN=2;DB;DP=28;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.65;SOR=6.736;VQSLOD=6.62;culprit=FS;GENE=GFRAL GT:AD:DP:GQ:PL 1/1:0,28:28:84:1211,84,0 -chr6 55264461 rs6913781 C T 236.8 PASS AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.83;SOR=4.174;VQSLOD=6.61;culprit=FS;GENE=GFRAL GT:AD:DP:GQ:PL 1/1:0,7:7:21:265,21,0 -chr6 55266394 rs1546297 T A 509.77 PASS AC=2;AF=1.0;AN=2;DB;DP=13;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.23;SOR=5.283;VQSLOD=7.14;culprit=FS;GENE=GFRAL GT:AD:DP:GQ:PL 1/1:0,13:13:39:538,39,0 -chr6 55266625 rs9370418 T C 5961.77 PASS AC=2;AF=1.0;AN=2;DB;DP=169;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.73;SOR=1.061;VQSLOD=5.15;culprit=FS;GENE=GFRAL GT:AD:DP:GQ:PL 1/1:0,169:169:99:5990,508,0 -chr6 55266722 rs12529201 C T 2018.77 PASS AC=2;AF=1.0;AN=2;DB;DP=54;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.58;SOR=6.593;VQSLOD=6.37;culprit=FS;GENE=GFRAL GT:AD:DP:GQ:PL 1/1:0,54:54:99:2047,162,0 -chr6 55266796 rs10948913 C T 23.79 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=1.733;ClippingRankSum=-0.898;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.48;QD=2.38;ReadPosRankSum=1.271;SOR=0.105;GENE=GFRAL GT:AD:DP:GQ:PL 0/1:8,2:10:52:52,0,252 -chr6 55275656 rs884360 A C 59.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=8.35;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 55294300 rs1393326 T A 60.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=63.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.09;SOR=1.179;VQSLOD=7.99;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:88,9,0 -chr6 55297178 rs1032766 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55334381 rs9382495 G A 53.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=8.86;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 55357373 rs4530860 A G 71.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.76;SOR=0.693;VQSLOD=6.89;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 -chr6 55358360 rs9475318 A G 91.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=1.179;VQSLOD=8.42;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:119,9,0 -chr6 55359142 rs70986720 A AC 44.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=0.693;VQSLOD=8.16;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 55359361 rs62407080 T A 121.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.467;ClippingRankSum=0.267;DB;DP=14;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.2;POSITIVE_TRAIN_SITE;QD=8.7;ReadPosRankSum=1.067;SOR=0.307;VQSLOD=4.49;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 0/1:9,5:14:99:150,0,312 -chr6 55360086 rs4538708 A G 530.77 PASS AC=2;AF=1.0;AN=2;DB;DP=13;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.72;SOR=5.283;VQSLOD=7.04;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,13:13:39:559,39,0 -chr6 55361878 rs9475319 T C 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=9.03;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 55365910 rs59233169 A ACT 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=7.75;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 55368931 rs4540264 T C 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.52;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 55378633 rs13206666 C T 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.78;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 55381262 rs6459082 G A 5521.77 PASS AC=2;AF=1.0;AN=2;DB;DP=145;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.56;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.7;SOR=4.22;VQSLOD=6.17;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,145:145:99:5550,436,0 -chr6 55381574 rs9464253 T G 460.77 PASS AC=2;AF=1.0;AN=2;DB;DP=13;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=48.24;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.44;SOR=5.283;VQSLOD=7.38;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,13:13:39:489,39,0 -chr6 55381594 rs9464254 T C 300.78 PASS AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.19;SOR=4.407;VQSLOD=7.05;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,8:8:24:329,24,0 -chr6 55392955 rs7743010 C G 87.28 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.13;SOR=0.693;VQSLOD=8.45;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,2:2:9:115,9,0 -chr6 55392956 rs7743274 G A 87.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.09;SOR=1.179;VQSLOD=7.93;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:115,9,0 -chr6 55406399 rs9367638 C T 1374.77 PASS AC=2;AF=1.0;AN=2;DB;DP=36;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.36;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.41;SOR=7.223;VQSLOD=6.72;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,36:36:99:1403,108,0 -chr6 55425387 rs9367641 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55431875 rs9464265 C G 60.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=0.693;VQSLOD=9.15;culprit=FS;GENE=HMGCLL1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:88,6,0 -chr6 55471178 rs4583976 G T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55494744 . C A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55509428 rs4504466 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55519639 rs10807498 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55545792 rs34899952 C T 572.77 PASS AC=2;AF=1.0;AN=2;DB;DP=15;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.12;SOR=5.549;VQSLOD=6.57;culprit=FS GT:AD:DP:GQ:PL 1/1:0,15:15:45:601,45,0 -chr6 55625041 rs3798845 G A 44.78 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.93;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.67;culprit=FS;GENE=BMP5 GT:AD:DP:GQ:PL 0/1:1,2:3:26:73,0,26 -chr6 55714314 rs62404968 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=BMP5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55730212 rs2021803 G A 169.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.969;ClippingRankSum=-0.648;DB;DP=22;FS=1.707;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.126;POSITIVE_TRAIN_SITE;QD=7.72;ReadPosRankSum=1.126;SOR=1.179;VQSLOD=2.48;culprit=QD;GENE=BMP5 GT:AD:DP:GQ:PL 0/1:14,8:22:99:198,0,496 -chr6 55739553 rs3734444 A G 5242.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=7.927;ClippingRankSum=0.832;DB;DP=341;FS=2.501;MLEAC=1;MLEAF=0.5;MQ=59.13;MQ0=0;MQRankSum=1.703;POSITIVE_TRAIN_SITE;QD=15.37;ReadPosRankSum=0.746;SOR=0.848;VQSLOD=1.42;culprit=DP;GENE=BMP5 GT:AD:DP:GQ:PL 0/1:176,162:338:99:5271,0,5457 -chr6 55848128 rs6911711 C T 57.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.09;SOR=1.179;VQSLOD=8.34;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:85,9,0 -chr6 55924214 rs3830813 TC T 169.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.073;ClippingRankSum=0.583;DB;DP=13;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.869;POSITIVE_TRAIN_SITE;QD=13.06;ReadPosRankSum=0.779;SOR=0.693;VQSLOD=6.26;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:6,6:12:99:207,0,206 -chr6 55926067 rs181810990 T A 105.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.55;ClippingRankSum=0.55;DB;DP=7;FS=3.68;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.55;QD=15.11;ReadPosRankSum=-0.937;SOR=2.494;VQSLOD=1.41;culprit=ReadPosRankSum;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:3,4:7:92:134,0,92 -chr6 55929347 rs2235735 T C 2151.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.816;ClippingRankSum=1.043;DB;DP=139;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.87;MQ0=0;MQRankSum=1.492;POSITIVE_TRAIN_SITE;QD=15.48;ReadPosRankSum=2.796;SOR=0.714;VQSLOD=2.9;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:63,75:138:99:2180,0,1872 -chr6 55929582 rs80177427 C T 195.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.989;ClippingRankSum=0.0;DB;DP=18;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.264;POSITIVE_TRAIN_SITE;QD=10.88;ReadPosRankSum=-0.996;SOR=0.368;VQSLOD=4.38;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:11,7:18:99:224,0,344 -chr6 55932035 rs138548441 A AT 3804.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=1.471;ClippingRankSum=-0.649;DB;DP=235;FS=5.07;MLEAC=1;MLEAF=0.5;MQ=60.13;MQ0=0;MQRankSum=-0.423;QD=16.19;ReadPosRankSum=-0.407;SOR=1.173;VQSLOD=-0.7158;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:134,100:234:99:3842,0,6908 -chr6 55932036 rs62406152 C T 3813.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-5.075;ClippingRankSum=1.08;DB;DP=238;FS=5.079;MLEAC=1;MLEAF=0.5;MQ=60.22;MQ0=0;MQRankSum=1.382;QD=16.02;ReadPosRankSum=-0.395;SOR=1.179;VQSLOD=-0.069;culprit=DP;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:136,102:238:99:3842,0,6908 -chr6 55932278 rs12209529 C T 994.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.948;ClippingRankSum=0.169;DB;DP=74;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.664;POSITIVE_TRAIN_SITE;QD=13.44;ReadPosRankSum=0.071;SOR=0.463;VQSLOD=4.42;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:42,32:74:99:1023,0,1552 -chr6 55932511 rs9396171 A G 64.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=1.179;VQSLOD=8.8;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,3:3:9:92,9,0 -chr6 55933942 rs12189567 A G 1295.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.173;ClippingRankSum=0.118;DB;DP=97;FS=4.397;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.361;POSITIVE_TRAIN_SITE;QD=13.36;ReadPosRankSum=-0.265;SOR=0.278;VQSLOD=2.33;culprit=DP;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:53,43:96:99:1324,0,1752 -chr6 55933987 rs12189571 A C 812.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.663;ClippingRankSum=-0.455;DB;DP=59;FS=5.997;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.675;POSITIVE_TRAIN_SITE;QD=13.78;ReadPosRankSum=1.539;SOR=2.506;VQSLOD=2.27;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:33,25:58:99:841,0,1009 -chr6 55935196 rs17218309 G A 45.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=2.303;VQSLOD=8.2;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 -chr6 55935617 rs41271338 T C 3245.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.63;ClippingRankSum=-1.316;DB;DP=211;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.833;POSITIVE_TRAIN_SITE;QD=15.38;ReadPosRankSum=-0.759;SOR=0.734;VQSLOD=1.27;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:104,107:211:99:3274,0,3061 -chr6 55935791 rs1028390 T C 301.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.261;ClippingRankSum=1.01;DB;DP=17;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.78;POSITIVE_TRAIN_SITE;QD=17.75;ReadPosRankSum=-0.241;SOR=0.804;VQSLOD=5.58;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:8,9:17:99:330,0,267 -chr6 55938839 rs4715576 G A 104.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.774;ClippingRankSum=-0.099;DB;DP=18;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.296;POSITIVE_TRAIN_SITE;QD=5.82;ReadPosRankSum=-0.591;SOR=0.616;VQSLOD=4.82;culprit=QD;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:13,5:18:99:133,0,453 -chr6 55942538 rs969513 G T 175.9 PASS AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.54;SOR=1.022;VQSLOD=6.0;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,5:5:15:204,15,0 -chr6 55942643 rs3065899 CAT C 36.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=63.51;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=12.24;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=2.76;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:1,2:3:41:74,0,41 -chr6 55942956 rs17218770 C G 1775.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.357;ClippingRankSum=0.32;DB;DP=106;FS=6.993;MLEAC=1;MLEAF=0.5;MQ=59.65;MQ0=0;MQRankSum=1.655;POSITIVE_TRAIN_SITE;QD=16.75;ReadPosRankSum=1.003;SOR=0.281;VQSLOD=1.69;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:50,56:106:99:1804,0,1640 -chr6 55943073 rs76049205 T C 470.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.873;ClippingRankSum=1.669;DB;DP=22;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=2.003;POSITIVE_TRAIN_SITE;QD=21.4;ReadPosRankSum=1.135;SOR=1.085;VQSLOD=4.22;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:9,13:22:99:499,0,281 -chr6 55943101 rs62404861 C A 242.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.366;ClippingRankSum=-0.34;DB;DP=15;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.34;POSITIVE_TRAIN_SITE;QD=16.18;ReadPosRankSum=1.324;SOR=0.818;VQSLOD=5.66;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:7,8:15:99:271,0,258 -chr6 55966027 rs12206920 C G 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.91;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 55966418 rs4379279 A G 640.77 PASS AC=2;AF=1.0;AN=2;DB;DP=16;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.42;SOR=5.67;VQSLOD=6.76;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,16:16:48:669,48,0 -chr6 55988619 rs41464152 T C 84.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=21.19;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=6.5;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:1,3:4:28:113,0,28 -chr6 55988796 rs150586735 TTA T 665.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.931;ClippingRankSum=-0.589;DB;DP=32;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=50.65;MQ0=0;MQRankSum=-1.804;POSITIVE_TRAIN_SITE;QD=20.8;ReadPosRankSum=0.285;SOR=0.957;VQSLOD=5.92;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:14,18:32:99:703,0,546 -chr6 55988837 . CT C 386.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.483;ClippingRankSum=-1.883;DP=57;FS=8.505;MLEAC=1;MLEAF=0.5;MQ=53.1;MQ0=0;MQRankSum=-0.083;POSITIVE_TRAIN_SITE;QD=6.78;ReadPosRankSum=0.276;SOR=2.91;VQSLOD=1.32;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:15,24:39:99:424,0,248 -chr6 55988932 rs41271844 T C 1723.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.801;ClippingRankSum=0.515;DB;DP=108;FS=2.53;MLEAC=1;MLEAF=0.5;MQ=57.92;MQ0=0;MQRankSum=0.871;POSITIVE_TRAIN_SITE;QD=15.96;ReadPosRankSum=0.465;SOR=0.446;VQSLOD=2.59;culprit=DP;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:50,57:107:99:1752,0,1593 -chr6 55989320 rs12210901 T C 81.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.537;ClippingRankSum=-0.406;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.406;POSITIVE_TRAIN_SITE;QD=13.63;ReadPosRankSum=0.406;SOR=0.693;VQSLOD=6.07;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:3,3:6:97:110,0,97 -chr6 55990773 rs146607719 GTTTAC G 82.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.358;ClippingRankSum=0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.21;MQ0=0;MQRankSum=-0.358;POSITIVE_TRAIN_SITE;QD=16.55;ReadPosRankSum=-1.231;SOR=1.022;VQSLOD=5.99;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:2,3:5:99:120,0,131 -chr6 56006672 rs10807510 C T 2289.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=6.297;ClippingRankSum=-0.222;DB;DP=137;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.209;POSITIVE_TRAIN_SITE;QD=16.71;ReadPosRankSum=0.316;SOR=0.641;VQSLOD=3.89;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:67,70:137:99:2318,0,1931 -chr6 56021453 rs33997736 CTA C 44.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=2.303;VQSLOD=8.3;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 56021870 rs111577315 T TAAA 789.73 PASS AC=2;AF=1.0;AN=2;DB;DP=29;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=52.38;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.23;SOR=5.892;VQSLOD=6.12;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,18:18:59:827,59,0 -chr6 56021985 rs1925180 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.13;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 56021991 rs1925181 C T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.99;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 56022644 rs9382583 C T 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.9;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 56023811 rs994667 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56029832 rs10708181 AT A 131.8 PASS AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=61.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=14.64;SOR=3.912;VQSLOD=6.42;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,6:6:18:169,18,0 -chr6 56031405 rs112307837 C T 257.41 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.348;ClippingRankSum=0.696;DB;DP=11;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.393;POSITIVE_TRAIN_SITE;QD=23.4;ReadPosRankSum=0.696;SOR=3.258;VQSLOD=5.3;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:1,9:10:8:285,0,8 -chr6 56033094 rs35471617 G A 1337.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.025;ClippingRankSum=-0.876;DB;DP=117;FS=1.69;MLEAC=1;MLEAF=0.5;MQ=59.84;MQ0=0;MQRankSum=1.143;POSITIVE_TRAIN_SITE;QD=11.43;ReadPosRankSum=1.054;SOR=0.91;VQSLOD=2.31;culprit=DP;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:70,47:117:99:1366,0,2112 -chr6 56037700 rs2397204 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56038131 rs9357892 A C 266.8 PASS AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=56.62;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.16;SOR=1.609;VQSLOD=6.49;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,7:7:21:295,21,0 -chr6 56038152 rs1925186 C G 388.77 PASS AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.39;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.093;VQSLOD=6.09;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,9:9:30:417,30,0 -chr6 56038178 rs9357893 G A 104.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.447;ClippingRankSum=0.633;DB;DP=11;FS=6.99;MLEAC=1;MLEAF=0.5;MQ=56.09;MQ0=0;MQRankSum=1.447;POSITIVE_TRAIN_SITE;QD=9.52;ReadPosRankSum=0.365;SOR=3.258;VQSLOD=1.97;culprit=QD;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:6,4:10:99:133,0,206 -chr6 56038210 rs77593705 G C 155.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.47;ClippingRankSum=-1.268;DB;DP=11;FS=5.441;MLEAC=1;MLEAF=0.5;MQ=58.29;MQ0=0;MQRankSum=0.336;POSITIVE_TRAIN_SITE;QD=14.16;ReadPosRankSum=0.47;SOR=0.662;VQSLOD=2.59;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 0/1:5,5:10:99:184,0,147 -chr6 56044578 rs2038149 T C 10645.77 PASS AC=2;AF=1.0;AN=2;DB;DP=271;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.32;SOR=1.041;VQSLOD=2.44;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,271:271:99:10674,815,0 -chr6 56045043 rs2038150 C A 1313.77 PASS AC=2;AF=1.0;AN=2;DB;DP=34;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.79;SOR=7.054;VQSLOD=6.76;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,33:33:99:1342,99,0 -chr6 56045393 rs6933151 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56076639 rs6939465 A C 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=9.31;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 56076688 rs6939632 C T 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=8.35;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 56078396 rs6908195 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56080842 rs4126555 A G 13.72 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=6.86;SOR=1.609;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 -chr6 56090871 rs3846924 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56094789 rs1925147 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56135778 . A T 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56141614 rs141389271 G GT 509.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.917;ClippingRankSum=0.694;DB;DP=108;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.93;MQ0=0;MQRankSum=0.858;QD=4.72;ReadPosRankSum=-0.709;SOR=0.467;VQSLOD=3.58;culprit=FS;GENE=DHFRP6,COL21A1 GT:AD:DP:GQ:PL 0/1:34,26:60:99:547,0,668 -chr6 56149855 rs9475651 G A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.83;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 56149857 rs4715605 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.22;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 56160179 rs4432980 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56163121 rs9396195 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56184256 rs4593354 T C 59.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.25;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 56231275 rs60251615 GT G 22.73 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=11.36;SOR=0.693;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:59,6,0 -chr6 56241523 rs6915564 T G 134.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.51;SOR=3.258;VQSLOD=7.79;culprit=FS;GENE=COL21A1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:162,12,0 -chr6 56271872 rs10456188 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56289250 rs623582 G A 62.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 56357668 rs376190394 CA C 95.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.642;ClippingRankSum=-0.049;DB;DP=93;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.6;MQ0=0;MQRankSum=1.135;QD=1.03;ReadPosRankSum=-0.148;SOR=0.156;VQSLOD=4.06;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:52,15:67:99:133,0,976 -chr6 56365814 rs4283892 A G 5670.77 PASS AC=2;AF=1.0;AN=2;DB;DP=169;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.86;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.55;SOR=2.647;VQSLOD=4.88;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 1/1:0,169:169:99:5699,507,0 -chr6 56371698 rs9296848 A G 6846.77 PASS AC=2;AF=1.0;AN=2;DB;DP=170;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.89;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.83;SOR=7.452;VQSLOD=5.12;culprit=QD;GENE=DST GT:AD:DP:GQ:PL 1/1:0,168:168:99:6875,506,0 -chr6 56373536 rs41271862 C T 2810.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-6.287;ClippingRankSum=-0.385;DB;DP=179;FS=1.419;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.394;POSITIVE_TRAIN_SITE;QD=15.7;ReadPosRankSum=1.719;SOR=0.556;VQSLOD=2.22;culprit=DP;GENE=DST GT:AD:DP:GQ:PL 0/1:86,93:179:99:2839,0,2900 -chr6 56374754 rs9296849 C A 3283.77 PASS AC=2;AF=1.0;AN=2;DB;DP=86;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.38;SOR=6.689;VQSLOD=6.47;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 1/1:0,86:86:99:3312,259,0 -chr6 56380064 rs5876514 CAT C 739.73 PASS AC=2;AF=1.0;AN=2;DB;DP=18;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=62.94;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.2;SOR=5.892;VQSLOD=6.33;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 1/1:0,18:18:54:777,54,0 -chr6 56381912 rs4715626 G A 9981.77 VQSRTrancheSNP99.00to99.90 AC=2;AF=1.0;AN=2;BaseQRankSum=1.706;ClippingRankSum=-1.538;DB;DP=273;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.49;MQ0=0;MQRankSum=-1.409;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=31.78;ReadPosRankSum=1.474;SOR=2.272;VQSLOD=-0.0057;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 1/1:1,267:268:99:10010,795,0 -chr6 56394173 rs9357922 T C 2768.77 PASS AC=2;AF=1.0;AN=2;DB;DP=70;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.67;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=8.526;VQSLOD=7.41;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 1/1:0,70:70:99:2797,210,0 -chr6 56395051 rs6939305 C A 2021.77 PASS AC=2;AF=1.0;AN=2;DB;DP=52;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.27;SOR=7.941;VQSLOD=7.06;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 1/1:0,52:52:99:2050,157,0 -chr6 56396694 rs34224935 CT C 39.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.85;SOR=0.693;VQSLOD=7.81;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 56399731 rs7758054 A T 964.77 PASS AC=2;AF=1.0;AN=2;DB;DP=25;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.5;SOR=6.518;VQSLOD=5.73;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 1/1:0,25:25:75:993,75,0 -chr6 56401999 rs4472350 G A 91.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=2.833;VQSLOD=9.11;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 1/1:0,3:3:9:119,9,0 -chr6 56403072 . G T 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=DST GT:AD:DP:GQ:PL 0/1:1,2:3:35:40,0,35 -chr6 56410533 . G T 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=DST GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56417282 rs4715630 C T 12421.77 PASS AC=2;AF=1.0;AN=2;DB;DP=331;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.93;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.31;SOR=1.081;VQSLOD=3.29;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 1/1:0,331:331:99:12450,995,0 -chr6 56417545 rs4715631 T C 10049.77 PASS AC=2;AF=1.0;AN=2;DB;DP=259;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.82;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.09;SOR=1.059;VQSLOD=4.04;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 1/1:0,259:259:99:10078,779,0 -chr6 56425284 rs2067543 A G 1201.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.751;ClippingRankSum=0.059;DB;DP=57;FS=3.927;MLEAC=1;MLEAF=0.5;MQ=59.67;MQ0=0;MQRankSum=-0.652;POSITIVE_TRAIN_SITE;QD=21.08;ReadPosRankSum=0.296;SOR=0.22;VQSLOD=2.01;culprit=QD;GENE=DST GT:AD:DP:GQ:PL 0/1:19,38:57:99:1230,0,587 -chr6 56425497 rs200368513 C A 36.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.37;SOR=2.303;VQSLOD=6.64;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 1/1:0,2:2:6:64,6,0 -chr6 56425900 rs1884284 G A 26.78 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=8.93;ReadPosRankSum=-0.736;SOR=1.179;GENE=DST GT:AD:DP:GQ:PL 0/1:1,2:3:35:55,0,35 -chr6 56425921 rs1884285 T A 80.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.92;ClippingRankSum=0.684;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.517;POSITIVE_TRAIN_SITE;QD=8.97;ReadPosRankSum=0.684;SOR=1.179;VQSLOD=4.63;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:4,5:9:99:118,0,116 -chr6 56425971 rs1884286 A G 590.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.542;ClippingRankSum=-0.814;DB;DP=30;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.374;POSITIVE_TRAIN_SITE;QD=19.69;ReadPosRankSum=-0.33;SOR=1.536;VQSLOD=5.66;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:10,20:30:99:619,0,310 -chr6 56426562 rs9357923 G A 403.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.202;ClippingRankSum=-0.527;DB;DP=23;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.837;POSITIVE_TRAIN_SITE;QD=17.56;ReadPosRankSum=-0.155;SOR=0.963;VQSLOD=5.73;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:10,13:23:99:432,0,331 -chr6 56426931 rs9367689 C T 2689.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.37;ClippingRankSum=0.043;DB;DP=192;FS=4.778;MLEAC=1;MLEAF=0.5;MQ=58.55;MQ0=0;MQRankSum=-0.486;POSITIVE_TRAIN_SITE;QD=14.01;ReadPosRankSum=2.114;SOR=0.409;VQSLOD=2.13;culprit=DP;GENE=DST GT:AD:DP:GQ:PL 0/1:95,96:191:99:2718,0,3023 -chr6 56427095 rs79573569 C CTGAGTGTTGAAA 1073.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.359;ClippingRankSum=0.523;DB;DP=57;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.02;MQ0=0;MQRankSum=-4.897;POSITIVE_TRAIN_SITE;QD=18.84;ReadPosRankSum=-1.568;SOR=0.483;VQSLOD=0.98;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:32,25:57:99:1111,0,1888 -chr6 56437465 rs1014309 T C 1445.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.09;ClippingRankSum=0.209;DB;DP=89;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.79;MQ0=0;MQRankSum=1.085;POSITIVE_TRAIN_SITE;QD=16.24;ReadPosRankSum=1.427;SOR=0.648;VQSLOD=5.2;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:45,43:88:99:1474,0,1510 -chr6 56437902 rs2144405 C T 1056.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.383;ClippingRankSum=0.809;DB;DP=66;FS=1.316;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.951;POSITIVE_TRAIN_SITE;QD=16.01;ReadPosRankSum=-1.516;SOR=0.461;VQSLOD=2.55;culprit=ReadPosRankSum;GENE=DST GT:AD:DP:GQ:PL 0/1:31,35:66:99:1085,0,1085 -chr6 56453346 rs6919941 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=DST GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56458332 . T A 301.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=2.437;ClippingRankSum=0.441;DP=28;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.13;MQ0=0;MQRankSum=-3.737;QD=10.78;ReadPosRankSum=-1.927;SOR=0.46;VQSLOD=-0.8078;culprit=MQRankSum;GENE=DST GT:AD:DP:GQ:PL 0/1:16,12:28:99:330,0,2663 -chr6 56458334 . G A 282.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=1.666;ClippingRankSum=0.476;DP=32;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.14;MQ0=0;MQRankSum=-3.134;QD=8.84;ReadPosRankSum=-0.992;SOR=0.26;VQSLOD=0.189;culprit=MQRankSum;GENE=DST GT:AD:DP:GQ:PL 0/1:21,11:32:99:311,0,3242 -chr6 56458337 . G A 260.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=1.343;ClippingRankSum=-0.083;DP=38;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.95;MQ0=0;MQRankSum=-3.199;QD=6.86;ReadPosRankSum=-0.878;SOR=0.134;VQSLOD=-0.4171;culprit=MQRankSum;GENE=DST GT:AD:DP:GQ:PL 0/1:28,10:38:99:289,0,3630 -chr6 56458338 . T A 215.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=4.133;ClippingRankSum=-0.659;DP=39;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.08;MQ0=0;MQRankSum=-3.522;NEGATIVE_TRAIN_SITE;QD=5.53;ReadPosRankSum=-2.3;SOR=0.126;VQSLOD=-2.429;culprit=MQRankSum;GENE=DST GT:AD:DP:GQ:PL 0/1:29,10:39:99:244,0,3725 -chr6 56458339 . AGGCT A 206.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=1.653;ClippingRankSum=-1.136;DP=43;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.56;MQ0=0;MQRankSum=-3.349;QD=4.81;ReadPosRankSum=-3.027;SOR=0.1;VQSLOD=-0.5999;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:33,10:43:99:244,0,3725 -chr6 56462840 rs9370541 G A 2994.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.431;ClippingRankSum=-1.553;DB;DP=213;FS=6.435;MLEAC=1;MLEAF=0.5;MQ=59.78;MQ0=0;MQRankSum=0.686;POSITIVE_TRAIN_SITE;QD=14.06;ReadPosRankSum=0.54;SOR=1.216;VQSLOD=2.1;culprit=DP;GENE=DST GT:AD:DP:GQ:PL 0/1:118,95:213:99:3023,0,3656 -chr6 56463410 rs4712138 T C 5519.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-7.361;ClippingRankSum=-0.682;DB;DP=398;FS=13.317;MLEAC=1;MLEAF=0.5;MQ=59.8;MQ0=0;MQRankSum=0.637;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=13.87;ReadPosRankSum=2.315;SOR=0.352;VQSLOD=-0.4795;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:208,189:397:99:5548,0,6660 -chr6 56466999 rs9382653 T G 75.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.21;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=15.15;ReadPosRankSum=1.231;SOR=1.022;VQSLOD=6.62;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:2,3:5:63:104,0,63 -chr6 56467586 rs11751914 G A 530.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.043;ClippingRankSum=1.304;DB;DP=35;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.403;POSITIVE_TRAIN_SITE;QD=15.16;ReadPosRankSum=1.601;SOR=0.641;VQSLOD=5.46;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:18,17:35:99:559,0,665 -chr6 56468238 rs9370543 G A 3348.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=8.795;ClippingRankSum=0.055;DB;DP=200;FS=1.921;MLEAC=1;MLEAF=0.5;MQ=59.77;MQ0=0;MQRankSum=0.619;POSITIVE_TRAIN_SITE;QD=16.74;ReadPosRankSum=2.983;SOR=0.871;VQSLOD=2.18;culprit=ReadPosRankSum;GENE=DST GT:AD:DP:GQ:PL 0/1:102,97:199:99:3377,0,3183 -chr6 56468537 rs9382656 T C 5633.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=8.003;ClippingRankSum=-2.016;DB;DP=287;FS=2.022;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.379;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=19.63;ReadPosRankSum=-1.151;SOR=0.827;VQSLOD=0.525;culprit=DP;GENE=DST GT:AD:DP:GQ:PL 0/1:124,162:286:99:5662,0,3728 -chr6 56470551 rs13194995 T A 4264.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.507;ClippingRankSum=-0.154;DB;DP=311;FS=0.415;MLEAC=1;MLEAF=0.5;MQ=59.87;MQ0=0;MQRankSum=-0.365;POSITIVE_TRAIN_SITE;QD=13.71;ReadPosRankSum=0.256;SOR=0.662;VQSLOD=1.73;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:169,141:310:99:4293,0,5525 -chr6 56470690 rs13209548 G A 4581.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.221;ClippingRankSum=0.043;DB;DP=298;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.85;MQ0=0;MQRankSum=-1.592;POSITIVE_TRAIN_SITE;QD=15.38;ReadPosRankSum=1.757;SOR=0.668;VQSLOD=1.27;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:151,147:298:99:4610,0,4504 -chr6 56471402 rs9382658 G A 5089.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.363;ClippingRankSum=0.422;DB;DP=342;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.581;POSITIVE_TRAIN_SITE;QD=14.88;ReadPosRankSum=0.721;SOR=0.676;VQSLOD=1.79;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:182,158:340:99:5118,0,6087 -chr6 56471995 rs16888055 C T 2905.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-6.315;ClippingRankSum=0.444;DB;DP=194;FS=5.194;MLEAC=1;MLEAF=0.5;MQ=59.69;MQ0=0;MQRankSum=0.379;POSITIVE_TRAIN_SITE;QD=14.98;ReadPosRankSum=1.462;SOR=1.052;VQSLOD=2.3;culprit=DP;GENE=DST GT:AD:DP:GQ:PL 0/1:97,95:192:99:2934,0,3313 -chr6 56476023 rs9370544 G A 43.78 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.59;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.14;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:1,2:3:27:72,0,27 -chr6 56476182 rs10643818 T TAAGTA 257.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.783;ClippingRankSum=0.79;DB;DP=31;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.17;MQ0=0;MQRankSum=-1.828;POSITIVE_TRAIN_SITE;QD=8.31;ReadPosRankSum=-0.384;SOR=0.132;VQSLOD=5.82;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:23,8:31:99:295,0,1187 -chr6 56476262 rs7747060 T C 1532.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.526;ClippingRankSum=-0.045;DB;DP=116;FS=1.204;MLEAC=1;MLEAF=0.5;MQ=58.89;MQ0=0;MQRankSum=-0.777;POSITIVE_TRAIN_SITE;QD=13.21;ReadPosRankSum=-0.453;SOR=0.898;VQSLOD=2.87;culprit=DP;GENE=DST GT:AD:DP:GQ:PL 0/1:67,49:116:99:1561,0,2190 -chr6 56476456 rs9396226 T A 997.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.112;ClippingRankSum=0.345;DB;DP=87;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.47;MQ0=0;MQRankSum=0.224;POSITIVE_TRAIN_SITE;QD=11.47;ReadPosRankSum=0.466;SOR=0.98;VQSLOD=4.8;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:34,44:78:99:1035,0,1041 -chr6 56482704 rs9396228 A C 747.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=5.823;ClippingRankSum=-0.173;DB;DP=72;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.209;POSITIVE_TRAIN_SITE;QD=10.39;ReadPosRankSum=2.168;SOR=0.735;VQSLOD=4.91;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:48,24:72:99:776,0,1600 -chr6 56482801 rs6459166 C G 2911.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.925;ClippingRankSum=0.679;DB;DP=217;FS=5.006;MLEAC=1;MLEAF=0.5;MQ=59.66;MQ0=0;MQRankSum=0.577;POSITIVE_TRAIN_SITE;QD=13.42;ReadPosRankSum=1.457;SOR=1.052;VQSLOD=2.17;culprit=DP;GENE=DST GT:AD:DP:GQ:PL 0/1:119,98:217:99:2940,0,3555 -chr6 56484758 rs2230862 C T 1769.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-6.905;ClippingRankSum=1.335;DB;DP=147;FS=6.412;MLEAC=1;MLEAF=0.5;MQ=56.34;MQ0=0;MQRankSum=1.822;POSITIVE_TRAIN_SITE;QD=12.04;ReadPosRankSum=0.721;SOR=0.357;VQSLOD=1.58;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:86,61:147:99:1798,0,2992 -chr6 56496649 rs10456737 A C 1638.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.101;ClippingRankSum=-1.291;DB;DP=80;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.42;MQ0=0;MQRankSum=-0.16;POSITIVE_TRAIN_SITE;QD=20.48;ReadPosRankSum=0.671;SOR=0.763;VQSLOD=5.14;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 0/1:29,51:80:99:1667,0,816 -chr6 56507135 rs1024195 T C 1136.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.677;ClippingRankSum=0.952;DB;DP=56;FS=1.927;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.207;POSITIVE_TRAIN_SITE;QD=20.3;ReadPosRankSum=-0.108;SOR=1.511;VQSLOD=2.71;culprit=QD;GENE=DST GT:AD:DP:GQ:PL 0/1:24,32:56:99:1165,0,749 -chr6 56701620 . G T 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=36.5;MQ0=0;QD=10.88;SOR=0.693;GENE=DST GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56736574 . TA T 49.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.817;ClippingRankSum=1.184;DP=26;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.89;MQ0=0;MQRankSum=0.531;QD=1.91;ReadPosRankSum=1.312;SOR=0.602;VQSLOD=4.48;culprit=FS;GENE=DST,RPL17P26 GT:AD:DP:GQ:PL 0/1:10,9:19:87:87,0,131 -chr6 56818706 rs986245 T C 816.77 PASS AC=2;AF=1.0;AN=2;DB;DP=24;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.03;SOR=2.925;VQSLOD=6.74;culprit=FS;GENE=DST GT:AD:DP:GQ:PL 1/1:0,24:24:72:845,72,0 -chr6 56827628 rs9349841 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=BEND6 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56846334 rs9396247 A G 342.78 PASS AC=2;AF=1.0;AN=2;DB;DP=9;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.76;SOR=4.615;VQSLOD=6.28;culprit=FS;GENE=BEND6 GT:AD:DP:GQ:PL 1/1:0,9:9:27:371,27,0 -chr6 56873069 rs6925819 T C 1050.77 PASS AC=2;AF=1.0;AN=2;DB;DP=30;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.45;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.57;SOR=3.912;VQSLOD=6.47;culprit=FS;GENE=BEND6 GT:AD:DP:GQ:PL 1/1:0,30:30:90:1079,90,0 -chr6 56893978 rs58747062 TC T 28.71 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=14.35;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:65,6,0 -chr6 56894940 rs34180205 CG C 106 PASS AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.2;SOR=3.258;VQSLOD=5.74;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:143,12,0 -chr6 56900699 rs3996934 C T 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=8.71;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 56917538 rs6926980 G A 2244.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.357;ClippingRankSum=0.056;DB;DP=147;FS=7.253;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.138;POSITIVE_TRAIN_SITE;QD=15.27;ReadPosRankSum=2.288;SOR=0.714;VQSLOD=2.13;culprit=FS;GENE=KIAA1586 GT:AD:DP:GQ:PL 0/1:74,73:147:99:2273,0,2345 -chr6 56919443 rs61740375 A G 752.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.392;ClippingRankSum=-0.128;DB;DP=52;FS=10.283;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.769;POSITIVE_TRAIN_SITE;QD=14.48;ReadPosRankSum=1.044;SOR=0.065;VQSLOD=1.36;culprit=FS;GENE=KIAA1586 GT:AD:DP:GQ:PL 0/1:27,25:52:99:781,0,941 -chr6 56963708 rs9367711 T G 789.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.396;ClippingRankSum=-0.682;DB;DP=55;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.513;POSITIVE_TRAIN_SITE;QD=14.36;ReadPosRankSum=0.295;SOR=0.729;VQSLOD=5.51;culprit=FS;GENE=ZNF451 GT:AD:DP:GQ:PL 0/1:27,28:55:99:818,0,939 -chr6 56994594 rs7758913 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=ZNF451 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56998023 rs3757296 A G 2007.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.613;ClippingRankSum=-0.822;DB;DP=133;FS=2.401;MLEAC=1;MLEAF=0.5;MQ=59.72;MQ0=0;MQRankSum=-0.518;POSITIVE_TRAIN_SITE;QD=15.1;ReadPosRankSum=-1.605;SOR=0.503;VQSLOD=2.33;culprit=ReadPosRankSum;GENE=ZNF451 GT:AD:DP:GQ:PL 0/1:64,67:131:99:2036,0,2080 -chr6 57006391 rs2273919 C T 310.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.573;ClippingRankSum=-0.38;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.55;MQ0=0;MQRankSum=1.356;POSITIVE_TRAIN_SITE;QD=19.42;ReadPosRankSum=2.007;SOR=1.244;VQSLOD=5.45;culprit=FS;GENE=ZNF451 GT:AD:DP:GQ:PL 0/1:6,10:16:99:339,0,197 -chr6 57006933 rs2273921 T C 1686.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.719;ClippingRankSum=0.791;DB;DP=136;FS=8.16;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.554;POSITIVE_TRAIN_SITE;QD=12.4;ReadPosRankSum=0.949;SOR=1.463;VQSLOD=2.01;culprit=FS;GENE=ZNF451 GT:AD:DP:GQ:PL 0/1:76,60:136:99:1715,0,2402 -chr6 57012930 rs3734738 C T 2118.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.567;ClippingRankSum=-0.086;DB;DP=161;FS=1.455;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.46;POSITIVE_TRAIN_SITE;QD=13.16;ReadPosRankSum=-1.077;SOR=0.558;VQSLOD=2.37;culprit=DP;GENE=ZNF451 GT:AD:DP:GQ:PL 0/1:87,74:161:99:2147,0,2812 -chr6 57048458 rs9885757 C T 476.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.695;ClippingRankSum=-0.057;DB;DP=32;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.28;MQ0=0;MQRankSum=0.057;POSITIVE_TRAIN_SITE;QD=14.9;ReadPosRankSum=0.019;SOR=0.693;VQSLOD=5.92;culprit=FS;GENE=BAG2 GT:AD:DP:GQ:PL 0/1:16,16:32:99:505,0,556 -chr6 57055354 rs1040461 C T 2987.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.147;ClippingRankSum=-2.243;DB;DP=178;FS=1.9;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.75;POSITIVE_TRAIN_SITE;QD=16.79;ReadPosRankSum=0.605;SOR=0.855;VQSLOD=2.11;culprit=DP;GENE=RAB23 GT:AD:DP:GQ:PL 0/1:81,97:178:99:3016,0,2448 -chr6 57059820 rs9357940 T G 252.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.739;ClippingRankSum=0.627;DB;DP=14;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.739;POSITIVE_TRAIN_SITE;QD=18.05;ReadPosRankSum=0.715;SOR=0.976;VQSLOD=6.0;culprit=FS;GENE=RAB23 GT:AD:DP:GQ:PL 0/1:6,8:14:99:281,0,187 -chr6 57074911 rs9357941 G A 404.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.359;ClippingRankSum=-0.103;DB;DP=26;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.462;POSITIVE_TRAIN_SITE;QD=15.57;ReadPosRankSum=-1.538;SOR=0.693;VQSLOD=5.41;culprit=FS;GENE=RAB23 GT:AD:DP:GQ:PL 0/1:13,13:26:99:433,0,497 -chr6 57097549 rs223304 T C 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=9.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 57106426 rs223289 T G 50.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=2.303;VQSLOD=8.94;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 57163494 rs7770252 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57182297 rs1019210 C T 63.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=6.13;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 57183869 . A T 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:34:40,0,34 -chr6 57188889 rs79594432 A T 460.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.171;ClippingRankSum=0.415;DB;DP=27;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.756;POSITIVE_TRAIN_SITE;QD=17.07;ReadPosRankSum=-0.512;SOR=0.922;VQSLOD=5.2;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:12,15:27:99:489,0,381 -chr6 57191021 rs11381745 A AG 1131.73 PASS AC=2;AF=1.0;AN=2;DB;DP=39;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=61.1;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.02;SOR=7.054;VQSLOD=6.03;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,33:33:99:1169,99,0 -chr6 57209749 rs9475860 C T 48.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=24.37;SOR=2.303;VQSLOD=6.73;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 57209802 rs1024706 T C 63.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.09;SOR=1.179;VQSLOD=7.21;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 57209865 rs5876534 GA G 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=7.46;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57209889 rs1024705 G T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.52;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57213782 rs7772897 A G 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57213785 rs7755104 T C 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.88;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57226182 rs17705499 C T 51.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=12.94;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=6.47;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,3:4:29:80,0,29 -chr6 57228571 rs12193422 G A 48.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=16.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.15;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:29:77,0,29 -chr6 57228598 rs6911124 A G 51.79 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.727;QD=12.95;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.09;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,3:4:23:80,0,23 -chr6 57228685 rs6911177 A G 123.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.38;ClippingRankSum=-0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.72;QD=20.63;ReadPosRankSum=-0.72;SOR=0.693;VQSLOD=4.71;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,4:6:99:152,0,126 -chr6 57228704 rs6934266 T G 46.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.358;QD=9.35;ReadPosRankSum=0.358;SOR=0.368;VQSLOD=4.4;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:3,2:5:75:75,0,154 -chr6 57228809 rs6911507 A C 50.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=16.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.92;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:32:79,0,32 -chr6 57231331 rs2079934 G T 32.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=63.51;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=10.92;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.36;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:32:61,0,32 -chr6 57231352 rs2397239 T C 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57231354 rs2397240 A G 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57232345 rs12200857 G A 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.44;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:28:40,0,28 -chr6 57232902 rs62417969 T G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57234078 rs9464454 A C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57243144 rs12201524 G A 49.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.026;QD=12.44;ReadPosRankSum=0.0;SOR=0.105;VQSLOD=4.21;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,154 -chr6 57243154 rs12201527 G A 49.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;QD=12.44;ReadPosRankSum=0.0;SOR=0.105;VQSLOD=4.91;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,154 -chr6 57244492 rs7759919 T C 24.78 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.572;ClippingRankSum=-1.067;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.572;QD=3.1;ReadPosRankSum=-1.067;SOR=0.169;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:6,2:8:53:53,0,209 -chr6 57244509 rs5011405 T G 34.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.589;ClippingRankSum=1.589;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.067;POSITIVE_TRAIN_SITE;QD=4.35;ReadPosRankSum=-0.572;SOR=0.169;VQSLOD=5.46;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:6,2:8:63:63,0,213 -chr6 57244672 rs5011404 G A 2178.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.306;ClippingRankSum=2.205;DB;DP=136;FS=2.003;MLEAC=1;MLEAF=0.5;MQ=59.83;MQ0=0;MQRankSum=-0.847;POSITIVE_TRAIN_SITE;QD=16.02;ReadPosRankSum=0.446;SOR=1.017;VQSLOD=2.92;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:66,70:136:99:2207,0,2213 -chr6 57244780 rs5011403 G A 3287.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.453;ClippingRankSum=0.408;DB;DP=235;FS=0.51;MLEAC=1;MLEAF=0.5;MQ=59.8;MQ0=0;MQRankSum=0.808;QD=13.99;ReadPosRankSum=0.963;SOR=0.634;VQSLOD=0.424;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:123,112:235:99:3316,0,3653 -chr6 57244830 rs5011402 T A 2187.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-4.318;ClippingRankSum=1.365;DB;DP=134;FS=4.341;MLEAC=1;MLEAF=0.5;MQ=59.83;MQ0=0;MQRankSum=-1.29;QD=16.33;ReadPosRankSum=0.292;SOR=0.162;VQSLOD=0.141;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:64,70:134:99:2216,0,2120 -chr6 57244893 rs5011401 T C 609.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.502;ClippingRankSum=-0.431;DB;DP=34;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-2.26;POSITIVE_TRAIN_SITE;QD=17.93;ReadPosRankSum=2.018;SOR=0.811;VQSLOD=4.32;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:16,18:34:99:638,0,509 -chr6 57244979 rs5011400 G A 91.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.358;ClippingRankSum=1.231;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.96;MQ0=0;MQRankSum=-1.231;QD=18.35;ReadPosRankSum=0.358;SOR=1.022;VQSLOD=4.54;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,3:5:99:120,0,137 -chr6 57244982 rs5011399 C T 91.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=-0.358;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.96;MQ0=0;MQRankSum=-1.231;QD=18.35;ReadPosRankSum=0.358;SOR=1.022;VQSLOD=4.34;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,3:5:99:120,0,137 -chr6 57246581 rs62415468 T A 183.85 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.742;ClippingRankSum=-0.742;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.62;MQ0=0;MQRankSum=-0.742;QD=26.26;ReadPosRankSum=-0.742;SOR=2.584;VQSLOD=3.61;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,6:7:17:212,0,17 -chr6 57246614 rs62415469 T C 379.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.371;ClippingRankSum=-2.285;DB;DP=15;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.718;QD=25.32;ReadPosRankSum=-1.371;SOR=1.911;VQSLOD=3.76;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:4,11:15:99:408,0,118 -chr6 57246638 rs6913328 C T 668.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.214;ClippingRankSum=-1.226;DB;DP=32;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.603;QD=20.9;ReadPosRankSum=1.654;SOR=1.284;VQSLOD=3.38;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:12,20:32:99:697,0,376 -chr6 57246708 rs6913779 G T 1443.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-8.155;ClippingRankSum=0.128;DB;DP=141;FS=4.59;MLEAC=1;MLEAF=0.5;MQ=59.75;MQ0=0;MQRankSum=-1.089;QD=10.24;ReadPosRankSum=-0.829;SOR=0.067;VQSLOD=-0.7831;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:92,49:141:99:1472,0,3506 -chr6 57246773 rs113849959 T TAGG 4992.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=0.588;ClippingRankSum=0.124;DB;DP=309;FS=5.829;MLEAC=1;MLEAF=0.5;MQ=57.08;MQ0=0;MQRankSum=-3.483;NEGATIVE_TRAIN_SITE;QD=16.16;ReadPosRankSum=1.26;SOR=1.145;VQSLOD=-2.405;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:174,127:301:99:5030,0,7083 -chr6 57246785 rs62415470 A C 5492.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=8.898;ClippingRankSum=-0.346;DB;DP=349;FS=1.043;MLEAC=1;MLEAF=0.5;MQ=57.28;MQ0=0;MQRankSum=-1.73;QD=15.74;ReadPosRankSum=1.758;SOR=0.781;VQSLOD=-0.7042;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:201,148:349:99:5521,0,7683 -chr6 57246815 rs6936571 T C 5593.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=6.746;ClippingRankSum=-1.594;DB;DP=416;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.57;MQ0=0;MQRankSum=-1.167;NEGATIVE_TRAIN_SITE;QD=13.45;ReadPosRankSum=-1.267;SOR=0.707;VQSLOD=-1.509;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:229,187:416:99:5622,0,7181 -chr6 57246878 rs61753604 T C 1938.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-1.885;ClippingRankSum=1.162;DB;DP=444;FS=0.65;MLEAC=1;MLEAF=0.5;MQ=58.81;MQ0=0;MQRankSum=-1.757;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=4.37;ReadPosRankSum=0.012;SOR=0.802;VQSLOD=-1.92;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:350,94:444:99:1967,0,13279 -chr6 57246884 rs6913546 A G 7065.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=3.408;ClippingRankSum=-0.389;DB;DP=440;FS=0.524;MLEAC=1;MLEAF=0.5;MQ=58.7;MQ0=0;MQRankSum=-2.305;NEGATIVE_TRAIN_SITE;QD=16.06;ReadPosRankSum=-1.094;SOR=0.63;VQSLOD=-2.286;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:227,212:439:99:7094,0,7015 -chr6 57246969 rs4256440 G A 4783.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-7.872;ClippingRankSum=0.62;DB;DP=347;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.69;MQ0=0;MQRankSum=-0.808;QD=13.79;ReadPosRankSum=-0.427;SOR=0.712;VQSLOD=-0.486;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:182,163:345:99:4812,0,6048 -chr6 57246982 rs4585567 G T 4000.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-7.751;ClippingRankSum=0.33;DB;DP=315;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.77;MQ0=0;MQRankSum=-0.546;QD=12.7;ReadPosRankSum=-0.935;SOR=0.712;VQSLOD=-0.553;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:174,139:313:99:4029,0,5824 -chr6 57247022 rs4382263 C T 3135.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-4.094;ClippingRankSum=-0.825;DB;DP=206;FS=9.797;MLEAC=1;MLEAF=0.5;MQ=59.1;MQ0=0;MQRankSum=0.277;QD=15.22;ReadPosRankSum=0.532;SOR=1.811;VQSLOD=-0.0767;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:108,98:206:99:3164,0,3645 -chr6 57247093 rs4499918 A T 892.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.606;ClippingRankSum=0.186;DB;DP=63;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.52;MQ0=0;MQRankSum=0.131;QD=14.17;ReadPosRankSum=-0.517;SOR=0.551;VQSLOD=2.59;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:34,29:63:99:921,0,1186 -chr6 57247108 rs4507595 G A 668.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.825;ClippingRankSum=0.298;DB;DP=53;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.24;MQ0=0;MQRankSum=-0.262;QD=12.62;ReadPosRankSum=0.406;SOR=0.416;VQSLOD=3.79;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:31,22:53:99:697,0,1110 -chr6 57247121 rs4310040 T C 577.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.37;ClippingRankSum=-1.834;DB;DP=43;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.82;MQ0=0;MQRankSum=-0.849;QD=13.44;ReadPosRankSum=-0.382;SOR=0.428;VQSLOD=3.58;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:25,18:43:99:606,0,856 -chr6 57259789 rs149275162 C A 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.23;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57259808 rs117189504 A T 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57259820 rs114240725 C T 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57260463 rs9475913 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57262992 rs2894847 A G 11.83 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=11.83;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0 -chr6 57263008 rs72871660 G C 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.87;SOR=2.303;VQSLOD=7.01;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 57284914 . G T 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57296209 rs78775831 G A 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=9.3;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57296216 rs80242777 C A 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=9.3;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57296249 rs72873542 C G 16.63 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=8.31;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:43,3,0 -chr6 57303056 rs62401712 T C 40.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=13.59;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=4.28;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:29:69,0,29 -chr6 57303102 rs62401713 A G 15.43 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=5.14;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:1:41,0,1 -chr6 57307716 rs60930046 T C 40.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=20.37;SOR=2.303;VQSLOD=6.63;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 57307784 rs60600423 C G 73.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=24.43;SOR=1.179;VQSLOD=5.3;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:101,9,0 -chr6 57309839 rs5003056 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57310132 rs73750278 C G 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57310138 rs73750279 C A 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57310284 rs9464491 A G 40.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=5.91;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 57310326 rs73750281 T G 52.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.47;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 -chr6 57310334 rs73750282 T C 52.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.59;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 -chr6 57315082 rs12204748 G A 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.37;SOR=0.693;VQSLOD=7.08;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 57325633 rs4715697 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57326248 rs2145339 A G 48.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=24.37;SOR=0.693;VQSLOD=7.07;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 57326568 rs9464502 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57330320 rs9382742 T C 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=9.34;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 57336157 rs9476010 G A 30.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.38;ClippingRankSum=0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.38;QD=5.13;ReadPosRankSum=0.0;SOR=0.693;VQSLOD=3.01;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:4,2:6:59:59,0,154 -chr6 57336243 rs9476012 G A 39.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.026;QD=9.94;ReadPosRankSum=0.0;SOR=0.105;VQSLOD=3.79;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,2:4:68:68,0,78 -chr6 57336279 rs9476013 C G 49.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.0;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;QD=12.44;ReadPosRankSum=0.0;SOR=0.105;VQSLOD=4.91;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,78 -chr6 57336284 rs9476014 A G 49.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.0;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;QD=12.44;ReadPosRankSum=1.026;SOR=0.105;VQSLOD=4.33;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,78 -chr6 57336340 rs1570072 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57342040 rs13219968 T C 63.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.09;SOR=1.179;VQSLOD=7.17;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 57345089 rs5024768 G C 40.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=6.41;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 57347208 . T TG 21.73 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.87;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:58,6,0 -chr6 57347800 rs34877937 C T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.09;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57347818 rs35142105 T G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.18;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57348150 rs34523439 G A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.16;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57348155 rs35239416 A T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.42;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57348440 rs34411188 A G 50.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=53.44;MQ0=0;MQRankSum=0.736;QD=16.92;ReadPosRankSum=-0.736;SOR=2.225;VQSLOD=1.11;culprit=ReadPosRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:28:79,0,28 -chr6 57348501 rs35975405 T C 71.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.34;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 -chr6 57348518 rs71221642 A G 71.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.4;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 -chr6 57348534 rs34153534 G A 107.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.69;SOR=1.179;VQSLOD=7.24;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 57348538 rs34509185 T G 107.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=35.33;SOR=1.179;VQSLOD=6.95;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 57349040 rs9476023 T C 93.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.09;SOR=1.179;VQSLOD=7.46;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:121,9,0 -chr6 57349257 rs9476024 C T 16.63 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=16.63;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:43,3,0 -chr6 57349280 rs12198778 A G 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=29.37;SOR=2.303;VQSLOD=7.09;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 57349405 rs9476025 A G 17.61 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=17.61;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:44,3,0 -chr6 57349426 rs9476026 C T 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.34;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57349572 rs6929331 A G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=9.11;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57349576 rs4715714 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=9.46;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57350134 rs9367752 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57353249 rs4715715 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57355968 rs35947597 T A 102.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.09;SOR=1.179;VQSLOD=7.02;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:130,9,0 -chr6 57355975 . C A 102.28 PASS AC=2;AF=1.0;AN=2;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.09;SOR=1.179;VQSLOD=5.89;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:130,9,0 -chr6 57355995 rs36115431 G A 102.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=34.09;SOR=1.179;VQSLOD=6.91;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:130,9,0 -chr6 57356611 rs9476033 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57358196 rs36181256 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57358870 rs4991170 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57358888 rs5876577 T TC 37.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.85;SOR=0.693;VQSLOD=7.35;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:74,6,0 -chr6 57362013 rs62399733 T C 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:31:40,0,31 -chr6 57362029 rs73752496 A G 52.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.73;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:74:81,0,74 -chr6 57362030 rs72877164 C T 52.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.56;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:74:81,0,74 -chr6 57362057 rs12526351 G A 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:36:40,0,36 -chr6 57364996 rs73755520 C T 32.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=-1.026;QD=8.19;ReadPosRankSum=0.0;SOR=0.105;VQSLOD=3.31;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,2:4:61:61,0,76 -chr6 57365151 rs5025370 T C 47.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=15.92;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=5.0;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:35:76,0,35 -chr6 57366534 rs4715718 G T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.68;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57366536 rs4715719 A T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.49;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57368219 rs62400883 G A 36.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=-0.736;QD=12.26;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.12;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:30:65,0,30 -chr6 57369510 rs62400894 A G 40.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=6.89;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 57371913 rs59066164 G A 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57371916 rs75944038 G A 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57371926 rs10949092 A T 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57371931 rs74978393 G A 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57371939 rs10949093 G A 53.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=26.87;SOR=0.693;VQSLOD=7.42;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 57371962 rs10949094 T A 48.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=24.37;SOR=0.693;VQSLOD=6.34;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 57372104 rs2024986 T C 162.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.512;ClippingRankSum=0.514;DB;DP=25;FS=5.528;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.091;QD=6.51;ReadPosRankSum=0.212;SOR=0.033;VQSLOD=0.457;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:18,7:25:99:191,0,669 -chr6 57372116 rs9382768 T C 752.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.259;ClippingRankSum=0.589;DB;DP=29;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.589;QD=25.96;ReadPosRankSum=-0.778;SOR=1.688;VQSLOD=2.67;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:9,20:29:99:781,0,276 -chr6 57372126 rs9396314 C G 253.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.17;ClippingRankSum=-1.868;DB;DP=35;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.51;POSITIVE_TRAIN_SITE;QD=7.25;ReadPosRankSum=0.698;SOR=0.129;VQSLOD=4.41;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:26,9:35:99:282,0,1018 -chr6 57372199 rs9382769 T C 3132.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=8.094;ClippingRankSum=0.441;DB;DP=131;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.12;MQ0=0;MQRankSum=-0.586;QD=23.91;ReadPosRankSum=-0.007;SOR=1.47;VQSLOD=1.39;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:46,85:131:99:3161,0,1398 -chr6 57372361 rs9382770 C A 10336.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-5.385;ClippingRankSum=-0.913;DB;DP=437;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.82;MQ0=0;MQRankSum=1.326;NEGATIVE_TRAIN_SITE;QD=23.65;ReadPosRankSum=0.567;SOR=0.72;VQSLOD=-2.151;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:149,287:436:99:10365,0,4146 -chr6 57372365 rs9396315 A G 3727.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-2.398;ClippingRankSum=-0.329;DB;DP=443;FS=0.613;MLEAC=1;MLEAF=0.5;MQ=58.84;MQ0=0;MQRankSum=3.315;NEGATIVE_TRAIN_SITE;QD=8.41;ReadPosRankSum=0.164;SOR=0.61;VQSLOD=-3.453;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:298,144:442:99:3756,0,10951 -chr6 57372374 rs68090917 CT C 3672.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=0.835;ClippingRankSum=0.028;DB;DP=420;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.5;MQ0=0;MQRankSum=0.217;POSITIVE_TRAIN_SITE;QD=8.74;ReadPosRankSum=0.275;SOR=0.674;VQSLOD=-0.1464;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:274,132:406:99:3710,0,8968 -chr6 57372436 rs9382771 G C 4364.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=4.675;ClippingRankSum=0.15;DB;DP=201;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.55;MQ0=0;MQRankSum=-2.89;NEGATIVE_TRAIN_SITE;QD=21.72;ReadPosRankSum=0.305;SOR=1.373;VQSLOD=-1.61;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:74,127:201:99:4393,0,2326 -chr6 57372437 rs79221898 C T 2323.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-9.294;ClippingRankSum=-0.543;DB;DP=202;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.44;MQ0=0;MQRankSum=0.03;QD=11.5;ReadPosRankSum=0.294;SOR=0.345;VQSLOD=0.165;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:123,79:202:99:2352,0,4259 -chr6 57372456 rs35141035 AT A 952.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.481;ClippingRankSum=0.386;DB;DP=149;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.01;MQ0=0;MQRankSum=-1.225;POSITIVE_TRAIN_SITE;QD=6.39;ReadPosRankSum=0.325;SOR=0.544;VQSLOD=3.61;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:65,50:115:99:990,0,1228 -chr6 57372480 rs79601039 A G 1090.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.462;ClippingRankSum=-0.042;DB;DP=82;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.03;MQ0=0;MQRankSum=0.276;QD=13.3;ReadPosRankSum=1.108;SOR=0.482;VQSLOD=3.82;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:46,36:82:99:1119,0,1889 -chr6 57372502 rs9349872 G A 894.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.559;ClippingRankSum=-0.64;DB;DP=44;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.08;MQ0=0;MQRankSum=-3.815;QD=20.34;ReadPosRankSum=-0.166;SOR=0.99;VQSLOD=0.816;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:19,25:44:99:923,0,664 -chr6 57372510 rs77697887 T G 453.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.557;ClippingRankSum=0.318;DB;DP=38;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=47.12;MQ0=0;MQRankSum=-3.102;QD=11.94;ReadPosRankSum=-1.226;SOR=0.307;VQSLOD=0.504;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:24,14:38:99:482,0,966 -chr6 57372514 rs77868044 T C 425.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.126;ClippingRankSum=0.397;DB;DP=32;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=48.03;MQ0=0;MQRankSum=-1.547;QD=13.31;ReadPosRankSum=-1.389;SOR=0.26;VQSLOD=2.8;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:21,11:32:99:454,0,927 -chr6 57372523 rs10706124 TG T 235.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.127;ClippingRankSum=0.381;DB;DP=28;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=48.16;MQ0=0;MQRankSum=-3.433;POSITIVE_TRAIN_SITE;QD=8.42;ReadPosRankSum=1.704;SOR=0.169;VQSLOD=2.42;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:20,8:28:99:273,0,858 -chr6 57372526 rs10635932 C CTTTA 238.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.25;ClippingRankSum=1.472;DB;DP=26;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=48.24;MQ0=0;MQRankSum=-3.139;POSITIVE_TRAIN_SITE;QD=9.18;ReadPosRankSum=1.694;SOR=0.202;VQSLOD=2.74;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:18,8:26:99:276,0,816 -chr6 57372583 rs9367754 C T 93.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.754;ClippingRankSum=-0.937;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.17;MQ0=0;MQRankSum=-0.937;QD=13.4;ReadPosRankSum=0.0;SOR=0.941;VQSLOD=4.53;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:3,4:7:99:122,0,108 -chr6 57372611 rs9382772 C T 32.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=-1.026;QD=8.19;ReadPosRankSum=0.0;SOR=0.693;VQSLOD=3.39;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,2:4:61:61,0,77 -chr6 57374364 rs75332238 C T 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:34:40,0,34 -chr6 57379671 rs4573085 C G 43.78 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.727;QD=10.95;ReadPosRankSum=0.727;SOR=0.916;VQSLOD=4.49;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,3:4:24:72,0,24 -chr6 57379715 rs2894901 T G 98.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;QD=24.51;SOR=1.609;VQSLOD=5.93;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:126,12,0 -chr6 57379745 rs9476056 G A 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=7.66;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 57384745 rs75634578 T C 40.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=6.95;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 57385801 rs4715735 A G 39.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=19.87;SOR=0.693;VQSLOD=6.75;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0 -chr6 57386904 rs149764231 GAGA G 43.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.58;ReadPosRankSum=-0.736;SOR=2.225;VQSLOD=2.5;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 -chr6 57389299 rs375498702 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57390094 rs12203268 T C 12.06 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:25:40,0,25 -chr6 57390107 rs200901455 CATCTGTT C 40.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=47.12;MQ0=0;MQRankSum=-1.026;QD=10.18;ReadPosRankSum=0.0;SOR=0.693;VQSLOD=5.2;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,78 -chr6 57390124 rs56102916 G C 111.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=27.76;SOR=0.693;VQSLOD=5.73;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:139,12,0 -chr6 57390134 rs75555855 C T 26.78 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=47.12;MQ0=0;MQRankSum=-1.026;QD=6.69;ReadPosRankSum=1.026;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,2:4:55:55,0,78 -chr6 57390168 rs78919924 C T 29.78 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=9.93;ReadPosRankSum=0.804;SOR=0.223;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:27:58,0,27 -chr6 57392874 rs927195 C T 110.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.0;ClippingRankSum=0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.72;QD=18.46;ReadPosRankSum=0.0;SOR=0.368;VQSLOD=4.73;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,4:6:61:139,0,61 -chr6 57392913 rs927194 T C 103.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.922;ClippingRankSum=-1.638;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.05;MQ0=0;MQRankSum=1.368;POSITIVE_TRAIN_SITE;QD=12.97;ReadPosRankSum=-0.922;SOR=0.693;VQSLOD=6.21;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:4,4:8:99:132,0,222 -chr6 57392921 rs62398963 T A 88.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.312;ClippingRankSum=-1.157;DB;DP=13;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.2;MQ0=0;MQRankSum=-0.231;QD=6.83;ReadPosRankSum=-0.386;SOR=0.223;VQSLOD=3.71;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:9,4:13:99:117,0,346 -chr6 57392963 rs927193 T C 531.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.951;ClippingRankSum=-0.11;DB;DP=29;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.39;MQ0=0;MQRankSum=0.68;QD=18.34;ReadPosRankSum=-0.811;SOR=0.906;VQSLOD=3.89;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:13,16:29:99:560,0,435 -chr6 57393029 rs77090024 T A 813.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=3.045;ClippingRankSum=0.061;DB;DP=76;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=-4.889;NEGATIVE_TRAIN_SITE;QD=10.71;ReadPosRankSum=2.576;SOR=0.201;VQSLOD=-3.073;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:52,24:76:99:842,0,2229 -chr6 57393034 rs75127850 G T 1008.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-5.248;ClippingRankSum=0.023;DB;DP=86;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.5;MQ0=0;MQRankSum=-5.58;NEGATIVE_TRAIN_SITE;QD=11.73;ReadPosRankSum=1.286;SOR=0.216;VQSLOD=-3.258;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:58,28:86:99:1037,0,2424 -chr6 57393040 rs74756458 A T 1158.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-2.499;ClippingRankSum=-1.753;DB;DP=96;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.21;MQ0=0;MQRankSum=-5.165;NEGATIVE_TRAIN_SITE;QD=12.07;ReadPosRankSum=1.667;SOR=0.229;VQSLOD=-3.001;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:64,32:96:99:1187,0,2672 -chr6 57393054 rs75725892 G A 1341.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=8.421;ClippingRankSum=0.555;DB;DP=120;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.42;MQ0=0;MQRankSum=-4.298;NEGATIVE_TRAIN_SITE;QD=11.18;ReadPosRankSum=1.283;SOR=1.179;VQSLOD=-2.209;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:81,39:120:99:1370,0,3620 -chr6 57393074 rs73752376 A G 1772.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=7.296;ClippingRankSum=0.236;DB;DP=171;FS=3.973;MLEAC=1;MLEAF=0.5;MQ=56.54;MQ0=0;MQRankSum=-2.664;NEGATIVE_TRAIN_SITE;QD=10.37;ReadPosRankSum=0.65;SOR=1.329;VQSLOD=-1.602;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:121,50:171:99:1801,0,5032 -chr6 57393092 rs73752377 T A 2197.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=2.298;ClippingRankSum=0.412;DB;DP=234;FS=2.43;MLEAC=1;MLEAF=0.5;MQ=56.7;MQ0=0;MQRankSum=-2.781;NEGATIVE_TRAIN_SITE;QD=9.39;ReadPosRankSum=-0.722;SOR=0.915;VQSLOD=-1.964;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:164,70:234:99:2226,0,6218 -chr6 57393125 rs927192 A G 7635.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=5.292;ClippingRankSum=-0.772;DB;DP=356;FS=5.93;MLEAC=1;MLEAF=0.5;MQ=57.99;MQ0=0;MQRankSum=0.055;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=21.45;ReadPosRankSum=-0.84;SOR=0.43;VQSLOD=-0.2175;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:129,227:356:99:7664,0,3693 -chr6 57393160 rs76686926 G A 2805.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-4.132;ClippingRankSum=0.139;DB;DP=395;FS=1.817;MLEAC=1;MLEAF=0.5;MQ=57.77;MQ0=0;MQRankSum=-1.496;NEGATIVE_TRAIN_SITE;QD=7.1;ReadPosRankSum=0.029;SOR=0.592;VQSLOD=-2.787;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:278,117:395:99:2834,0,8784 -chr6 57393199 rs2397502 C A 3769.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-6.119;ClippingRankSum=1.716;DB;DP=344;FS=1.419;MLEAC=1;MLEAF=0.5;MQ=58.31;MQ0=0;MQRankSum=2.244;NEGATIVE_TRAIN_SITE;QD=10.96;ReadPosRankSum=0.093;SOR=0.606;VQSLOD=-1.342;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:226,118:344:99:3798,0,8416 -chr6 57393216 rs2397503 G T 6455.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-7.047;ClippingRankSum=0.677;DB;DP=273;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.46;MQ0=0;MQRankSum=-1.274;NEGATIVE_TRAIN_SITE;QD=23.65;ReadPosRankSum=0.802;SOR=0.672;VQSLOD=-1.677;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:112,161:273:99:6484,0,4010 -chr6 57393222 rs111989160 A G 2124.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=6.075;ClippingRankSum=0.447;DB;DP=254;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.63;MQ0=0;MQRankSum=-0.081;NEGATIVE_TRAIN_SITE;QD=8.37;ReadPosRankSum=1.798;SOR=0.705;VQSLOD=-1.47;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:191,63:254:99:2153,0,7932 -chr6 57393228 rs112156516 G A 2056.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=7.272;ClippingRankSum=-0.141;DB;DP=242;FS=2.168;MLEAC=1;MLEAF=0.5;MQ=58.56;MQ0=0;MQRankSum=0.518;NEGATIVE_TRAIN_SITE;QD=8.5;ReadPosRankSum=2.889;SOR=1.002;VQSLOD=-1.477;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:182,60:242:99:2085,0,7456 -chr6 57393278 rs75909609 T C 978.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=7.163;ClippingRankSum=1.948;DB;DP=126;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.86;MQ0=0;MQRankSum=0.294;QD=7.77;ReadPosRankSum=0.566;SOR=0.428;VQSLOD=1.81;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:93,33:126:99:1007,0,3194 -chr6 57393323 rs12198995 T C 122.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.995;ClippingRankSum=-0.894;DB;DP=63;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.03;MQ0=0;MQRankSum=-1.012;QD=1.95;ReadPosRankSum=0.953;SOR=0.033;VQSLOD=0.768;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:54,9:63:99:151,0,2049 -chr6 57393329 rs76564922 G T 491.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.488;ClippingRankSum=-0.148;DB;DP=58;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.67;MQ0=0;MQRankSum=1.018;QD=8.48;ReadPosRankSum=0.478;SOR=0.145;VQSLOD=3.43;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:42,16:58:99:520,0,1666 -chr6 57393337 rs200714656 T TA 779.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.011;ClippingRankSum=0.247;DB;DP=47;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.61;MQ0=0;MQRankSum=-1.517;POSITIVE_TRAIN_SITE;QD=16.59;ReadPosRankSum=-0.957;SOR=0.446;VQSLOD=5.5;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:27,20:47:99:817,0,1052 -chr6 57393338 rs2397504 T A 1418.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-3.401;ClippingRankSum=0.911;DB;DP=45;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.36;MQ0=0;MQRankSum=-1.809;NEGATIVE_TRAIN_SITE;QD=31.53;ReadPosRankSum=-1.578;SOR=2.059;VQSLOD=-0.2208;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:12,33:45:99:1447,0,396 -chr6 57393350 rs2397505 G A 577.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.397;ClippingRankSum=-0.51;DB;DP=37;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=52.72;MQ0=0;MQRankSum=-2.8;QD=15.62;ReadPosRankSum=-1.686;SOR=0.395;VQSLOD=1.1;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:22,15:37:99:606,0,861 -chr6 57393407 rs374979361 C T 67.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.683;ClippingRankSum=-0.573;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.248;QD=7.53;ReadPosRankSum=-0.248;SOR=0.283;VQSLOD=4.48;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:6,3:9:96:96,0,194 -chr6 57393519 rs62398965 A G 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=7.5;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 57393716 rs2397508 G A 53.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.87;SOR=2.303;VQSLOD=7.44;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 57394939 rs11963080 C T 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.21;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57395058 rs12202626 T C 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.37;SOR=2.303;VQSLOD=7.08;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 57395077 rs12195527 C G 61.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=30.87;SOR=2.303;VQSLOD=7.52;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:89,6,0 -chr6 57395396 rs74519885 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57396165 rs6924765 G A 52.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=3.82;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:78:81,0,78 -chr6 57396173 rs79246915 G T 52.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=-0.736;SOR=0.223;VQSLOD=4.76;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:78:81,0,78 -chr6 57397866 rs57276498 T TA 68.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.72;ClippingRankSum=0.0;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.82;MQ0=0;MQRankSum=-0.72;POSITIVE_TRAIN_SITE;QD=11.46;ReadPosRankSum=0.72;SOR=1.329;VQSLOD=5.96;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,4:6:38:106,0,38 -chr6 57397944 rs7770986 A G 201.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.659;ClippingRankSum=-0.183;DB;DP=34;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.28;MQ0=0;MQRankSum=0.183;QD=5.93;ReadPosRankSum=-0.386;SOR=0.392;VQSLOD=2.5;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:26,8:34:99:230,0,866 -chr6 57397982 rs7771127 C A 876.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.945;ClippingRankSum=-0.215;DB;DP=57;FS=3.087;MLEAC=1;MLEAF=0.5;MQ=56.94;MQ0=0;MQRankSum=-1.269;QD=15.38;ReadPosRankSum=0.567;SOR=0.197;VQSLOD=1.24;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:29,28:57:99:905,0,992 -chr6 57398008 rs7771257 C T 1863.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-6.114;ClippingRankSum=-0.432;DB;DP=91;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.21;MQ0=0;MQRankSum=-1.126;QD=20.48;ReadPosRankSum=-0.093;SOR=0.232;VQSLOD=3.03;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:44,46:90:99:1892,0,1700 -chr6 57398009 rs7771114 A G 1863.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=5.944;ClippingRankSum=0.703;DB;DP=92;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.26;MQ0=0;MQRankSum=-3.03;POSITIVE_TRAIN_SITE;QD=20.26;ReadPosRankSum=-0.203;SOR=0.241;VQSLOD=3.1;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:44,47:91:99:1892,0,1700 -chr6 57398028 rs67286646 TG T 832.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.812;ClippingRankSum=-0.912;DB;DP=148;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.11;MQ0=0;MQRankSum=0.437;POSITIVE_TRAIN_SITE;QD=5.63;ReadPosRankSum=-0.426;SOR=0.853;VQSLOD=3.92;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:107,40:147:99:870,0,4153 -chr6 57398047 rs76081480 A C 1782.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=7.353;ClippingRankSum=-0.762;DB;DP=191;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.74;MQ0=0;MQRankSum=-2.177;NEGATIVE_TRAIN_SITE;QD=9.33;ReadPosRankSum=-1.084;SOR=0.701;VQSLOD=-1.736;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:127,63:190:99:1811,0,4583 -chr6 57398058 rs7771283 C G 1588.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-4.421;ClippingRankSum=0.238;DB;DP=230;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.8;MQ0=0;MQRankSum=1.141;NEGATIVE_TRAIN_SITE;QD=6.91;ReadPosRankSum=-1.687;SOR=0.435;VQSLOD=-2.531;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:168,61:229:99:1617,0,5971 -chr6 57398081 rs7753294 T G 5599.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=8.745;ClippingRankSum=0.077;DB;DP=263;FS=27.103;MLEAC=1;MLEAF=0.5;MQ=54.71;MQ0=0;MQRankSum=-4.145;NEGATIVE_TRAIN_SITE;QD=21.29;ReadPosRankSum=2.243;SOR=3.663;VQSLOD=-1.976;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:103,159:262:99:5628,0,3075 -chr6 57398117 rs139574925 T TA 2948.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-1.101;ClippingRankSum=1.493;DB;DP=361;FS=2.214;MLEAC=1;MLEAF=0.5;MQ=54.59;MQ0=0;MQRankSum=-1.42;NEGATIVE_TRAIN_SITE;QD=8.17;ReadPosRankSum=-1.614;SOR=0.901;VQSLOD=-2.236;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:262,99:361:99:2986,0,10807 -chr6 57398118 rs147643173 G T 2951.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-8.611;ClippingRankSum=0.472;DB;DP=366;FS=1.357;MLEAC=1;MLEAF=0.5;MQ=54.39;MQ0=0;MQRankSum=-1.61;NEGATIVE_TRAIN_SITE;QD=8.06;ReadPosRankSum=-1.741;SOR=0.841;VQSLOD=-2.741;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:265,101:366:99:2980,0,10921 -chr6 57398154 rs80081867 T C 9900.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.712;ClippingRankSum=-1.351;DB;DP=417;FS=3.795;MLEAC=1;MLEAF=0.5;MQ=52.44;MQ0=0;MQRankSum=-5.322;NEGATIVE_TRAIN_SITE;QD=23.74;ReadPosRankSum=0.785;SOR=1.039;VQSLOD=-2.613;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:170,247:417:99:9929,0,6569 -chr6 57398157 rs9476080 A G 10031.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=11.939;ClippingRankSum=-0.67;DB;DP=420;FS=5.63;MLEAC=1;MLEAF=0.5;MQ=52.56;MQ0=0;MQRankSum=-6.161;NEGATIVE_TRAIN_SITE;QD=23.89;ReadPosRankSum=1.335;SOR=1.089;VQSLOD=-2.877;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:174,246:420:99:10060,0,6871 -chr6 57398163 rs9476081 A G 9691.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-5.386;ClippingRankSum=-0.317;DB;DP=428;FS=7.782;MLEAC=1;MLEAF=0.5;MQ=52.95;MQ0=0;MQRankSum=-7.057;NEGATIVE_TRAIN_SITE;QD=22.64;ReadPosRankSum=2.15;SOR=1.207;VQSLOD=-3.25;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:182,246:428:99:9720,0,6877 -chr6 57398186 rs147954160 G GA 3146.73 VQSRTrancheINDEL99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=1.394;ClippingRankSum=0.081;DB;DP=466;FS=0.612;MLEAC=1;MLEAF=0.5;MQ=53.38;MQ0=0;MQRankSum=-5.529;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=6.75;ReadPosRankSum=-0.584;SOR=0.648;VQSLOD=-3.838;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:331,119:450:99:3184,0,13464 -chr6 57398201 rs62398997 T C 9311.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=1.718;ClippingRankSum=0.323;DB;DP=477;FS=1.13;MLEAC=1;MLEAF=0.5;MQ=53.38;MQ0=0;MQRankSum=-2.722;NEGATIVE_TRAIN_SITE;QD=19.52;ReadPosRankSum=0.869;SOR=0.576;VQSLOD=-2.548;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:235,242:477:99:9340,0,8506 -chr6 57398207 rs71214816 G T 3201.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-4.739;ClippingRankSum=0.609;DB;DP=476;FS=3.961;MLEAC=1;MLEAF=0.5;MQ=53.59;MQ0=0;MQRankSum=-5.623;NEGATIVE_TRAIN_SITE;QD=6.73;ReadPosRankSum=0.211;SOR=0.475;VQSLOD=-3.396;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:358,113:471:99:3230,0,14267 -chr6 57398226 rs77436138 T G 5638.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=6.88;ClippingRankSum=1.585;DB;DP=474;FS=4.176;MLEAC=1;MLEAF=0.5;MQ=55.11;MQ0=0;MQRankSum=-0.678;NEGATIVE_TRAIN_SITE;QD=11.9;ReadPosRankSum=-1.594;SOR=0.924;VQSLOD=-2.787;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:202,185:387:99:5667,0,7682 -chr6 57398264 rs62398998 A G 10505.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=7.8;ClippingRankSum=0.363;DB;DP=483;FS=5.181;MLEAC=1;MLEAF=0.5;MQ=56.66;MQ0=0;MQRankSum=-3.599;NEGATIVE_TRAIN_SITE;QD=21.75;ReadPosRankSum=1.128;SOR=0.919;VQSLOD=-2.719;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:185,297:482:99:10534,0,5426 -chr6 57398270 rs62398999 C T 3777.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-8.082;ClippingRankSum=1.817;DB;DP=482;FS=4.566;MLEAC=1;MLEAF=0.5;MQ=56.75;MQ0=0;MQRankSum=-2.615;NEGATIVE_TRAIN_SITE;QD=7.84;ReadPosRankSum=0.627;SOR=1.059;VQSLOD=-3.182;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:338,143:481:99:3806,0,12584 -chr6 57398335 rs4715745 A T 7297.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=0.878;ClippingRankSum=-0.623;DB;DP=391;FS=18.28;MLEAC=1;MLEAF=0.5;MQ=56.94;MQ0=0;MQRankSum=-1.096;NEGATIVE_TRAIN_SITE;QD=18.66;ReadPosRankSum=0.479;SOR=1.573;VQSLOD=-1.998;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:151,240:391:99:7326,0,4341 -chr6 57398385 rs11455120 A AT 2033.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-4.004;ClippingRankSum=-0.159;DB;DP=270;FS=2.505;MLEAC=1;MLEAF=0.5;MQ=57.95;MQ0=0;MQRankSum=1.708;POSITIVE_TRAIN_SITE;QD=7.53;ReadPosRankSum=2.608;SOR=1.265;VQSLOD=-0.3154;culprit=ReadPosRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:165,71:236:99:2071,0,7214 -chr6 57398395 rs78658694 A T 1426.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=5.633;ClippingRankSum=-0.557;DB;DP=246;FS=2.513;MLEAC=1;MLEAF=0.5;MQ=58.16;MQ0=0;MQRankSum=-1.385;NEGATIVE_TRAIN_SITE;QD=5.8;ReadPosRankSum=2.107;SOR=1.287;VQSLOD=-2.484;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:170,67:237:99:1455,0,7359 -chr6 57398412 rs6937166 A G 1614.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=5.113;ClippingRankSum=0.84;DB;DP=201;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.23;MQ0=0;MQRankSum=0.045;NEGATIVE_TRAIN_SITE;QD=8.03;ReadPosRankSum=-0.11;SOR=0.142;VQSLOD=-1.257;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:145,56:201:99:1643,0,5481 -chr6 57398491 rs6937368 C T 90.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.276;ClippingRankSum=0.17;DB;DP=40;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.42;MQ0=0;MQRankSum=-0.019;QD=2.27;ReadPosRankSum=-0.511;SOR=0.039;VQSLOD=1.26;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:34,6:40:99:119,0,1359 -chr6 57398503 rs4388290 A G 387.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.279;ClippingRankSum=-0.151;DB;DP=36;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.36;MQ0=0;MQRankSum=-0.319;QD=10.77;ReadPosRankSum=-0.319;SOR=0.239;VQSLOD=2.63;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:24,12:36:99:416,0,1055 -chr6 57398517 rs4400219 C A 314.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.503;ClippingRankSum=0.37;DB;DP=31;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.25;MQ0=0;MQRankSum=-0.196;QD=10.15;ReadPosRankSum=0.849;SOR=0.173;VQSLOD=3.45;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:22,9:31:99:343,0,999 -chr6 57398587 rs4506046 A G 226.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.635;ClippingRankSum=-0.831;DB;DP=12;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.977;QD=18.9;ReadPosRankSum=1.977;SOR=1.022;VQSLOD=3.22;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:5,7:12:99:255,0,157 -chr6 57398921 . T C 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:36:40,0,36 -chr6 57398943 rs12203062 C T 29.77 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.0;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;QD=7.44;ReadPosRankSum=-1.026;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,2:4:58:58,0,78 -chr6 57404528 rs12528027 A G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.24;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57404529 rs71221626 G C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.19;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57404548 rs6934525 T C 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57404559 rs6911998 G T 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57409216 rs487488 T C 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57409238 rs7757807 T G 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57409250 rs28431347 T A 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57409360 rs7775846 A C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.44;MQ0=0;QD=7.26;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57414331 rs522176 A G 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.28;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57414352 rs522107 G T 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57414355 rs577952 G A 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57419091 rs11362490 AG A 32.71 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=16.35;SOR=2.303;VQSLOD=8.34;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 -chr6 57419145 rs482977 T C 101.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.26;SOR=0.693;VQSLOD=7.58;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:129,12,0 -chr6 57419169 rs482916 C T 96.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.09;SOR=1.179;VQSLOD=6.81;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:124,9,0 -chr6 57419203 rs28444227 T A 84.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.09;SOR=1.179;VQSLOD=6.21;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:112,9,0 -chr6 57419529 rs5011343 C T 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57419548 rs5011342 G A 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=29.24;SOR=1.609;VQSLOD=4.67;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:6:70,6,0 -chr6 57419564 rs5011341 G A 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.6;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57419593 rs5000703 G T 60.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=20.09;SOR=1.179;VQSLOD=6.82;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:88,9,0 -chr6 57419621 rs5000702 C A 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.37;SOR=0.693;VQSLOD=7.18;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 57420055 rs973971 A T 47.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=23.87;SOR=0.693;VQSLOD=7.29;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 57420085 rs10678736 T TGCAATA 43.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.58;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=2.61;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 -chr6 57420331 rs536921 A G 45.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;QD=11.44;ReadPosRankSum=1.026;SOR=0.105;VQSLOD=4.6;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,2:4:33:74,0,33 -chr6 57420394 rs3903673 C G 39.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=1.231;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.358;QD=7.95;ReadPosRankSum=1.231;SOR=1.609;VQSLOD=2.43;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:3,2:5:68:68,0,116 -chr6 57429628 rs9476125 T G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.39;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57429632 rs13200513 C A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.12;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57429655 rs13200414 A T 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57429863 rs12194179 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57430291 rs12209094 A G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.61;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57430302 rs12195853 G C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=5.78;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57430787 rs9382792 A G 66.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=22.09;SOR=1.179;VQSLOD=5.69;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:94,9,0 -chr6 57430868 rs9396334 C T 14.68 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=14.68;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:41,3,0 -chr6 57431267 rs2397534 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57436741 rs6924004 C A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57437720 rs519735 A G 47.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=23.87;SOR=0.693;VQSLOD=6.98;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 57437853 rs13212334 A G 12.06 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:25:40,0,25 -chr6 57438133 rs1174361 T C 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57438139 rs1174362 C T 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57438156 rs78245671 T C 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.19;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57440169 rs581096 G A 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57440174 rs581102 T C 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57440196 rs581193 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.05;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57440211 rs581228 T A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=9.37;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57442438 rs5005193 C G 60.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=30.37;SOR=2.303;VQSLOD=7.36;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:88,6,0 -chr6 57442463 rs5005192 T G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.31;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57442488 rs4715782 A G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.25;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57442506 rs5005191 A G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.49;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57442507 rs5005190 A G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.99;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57443228 rs6913239 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57443255 rs1855414 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57447972 rs4715787 T G 53.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.87;SOR=2.303;VQSLOD=6.49;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 57454558 rs9357983 C A 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57454567 rs62399084 A T 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57454589 rs9357984 A G 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.54;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57454920 rs9357986 C T 55.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;QD=18.43;SOR=1.179;VQSLOD=5.05;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:83,9,0 -chr6 57455443 rs7766809 A G 98.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=32.76;SOR=1.179;VQSLOD=6.98;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:126,9,0 -chr6 57456136 rs4596481 T C 13.72 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=6.86;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 -chr6 57456931 rs79510351 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57456963 rs75987787 T C 107.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.05;SOR=1.179;VQSLOD=6.12;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 57456968 rs78473260 G A 107.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.4;SOR=1.179;VQSLOD=6.89;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 57457564 rs3805802 A G 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=8.6;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 57461356 rs62399146 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57463643 rs6905367 A G 45.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=22.87;SOR=2.303;VQSLOD=7.58;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 -chr6 57466787 rs6924157 G C 81.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.358;ClippingRankSum=-1.231;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.358;QD=16.35;ReadPosRankSum=0.358;SOR=0.223;VQSLOD=5.23;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,3:5:59:110,0,59 -chr6 57466812 rs78692044 T A 28.77 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.72;ClippingRankSum=0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.04;MQ0=0;MQRankSum=-0.72;QD=4.8;ReadPosRankSum=-0.72;SOR=1.179;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:4,2:6:57:57,0,146 -chr6 57466836 rs11411187 A AC 203.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.067;ClippingRankSum=1.589;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.05;MQ0=0;MQRankSum=0.572;POSITIVE_TRAIN_SITE;QD=25.47;ReadPosRankSum=-1.067;SOR=0.693;VQSLOD=5.99;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,6:8:57:241,0,57 -chr6 57466844 rs12197381 G A 64.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.573;ClippingRankSum=-0.573;DB;DP=9;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=57.39;MQ0=0;MQRankSum=0.248;QD=7.2;ReadPosRankSum=0.248;SOR=0.045;VQSLOD=0.706;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:6,3:9:93:93,0,212 -chr6 57466871 rs79082382 G A 111.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.793;ClippingRankSum=0.244;DB;DP=12;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=-2.141;QD=9.31;ReadPosRankSum=-0.529;SOR=0.446;VQSLOD=2.61;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:7,5:12:99:140,0,269 -chr6 57466891 rs12210717 A T 431.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.484;ClippingRankSum=-0.698;DB;DP=21;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.45;MQ0=0;MQRankSum=-0.611;QD=20.56;ReadPosRankSum=0.349;SOR=0.941;VQSLOD=3.93;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:5,15:20:99:460,0,165 -chr6 57466915 rs12205876 T A 732.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.992;ClippingRankSum=1.449;DB;DP=28;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.62;MQ0=0;MQRankSum=0.839;QD=26.17;ReadPosRankSum=1.297;SOR=0.402;VQSLOD=2.6;culprit=ReadPosRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:8,20:28:99:761,0,252 -chr6 57466922 rs2894917 T C 1572.77 PASS AC=2;AF=1.0;AN=2;DB;DP=36;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.39;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.29;SOR=4.921;VQSLOD=6.55;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,36:36:99:1601,111,0 -chr6 57466957 rs9885746 C T 515.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=2.903;ClippingRankSum=-0.774;DB;DP=69;FS=3.021;MLEAC=1;MLEAF=0.5;MQ=57.62;MQ0=0;MQRankSum=-0.787;QD=7.47;ReadPosRankSum=-0.192;SOR=0.154;VQSLOD=-0.3023;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:49,20:69:99:544,0,2169 -chr6 57466958 rs12212128 A G 1712.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.269;ClippingRankSum=0.064;DB;DP=74;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.81;MQ0=0;MQRankSum=-1.391;QD=23.15;ReadPosRankSum=-0.906;SOR=0.355;VQSLOD=2.47;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:24,50:74:99:1741,0,776 -chr6 57466969 rs12212129 A G 1088.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=6.62;ClippingRankSum=-0.34;DB;DP=83;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.03;MQ0=0;MQRankSum=-0.237;QD=13.12;ReadPosRankSum=-0.386;SOR=0.362;VQSLOD=3.55;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:50,33:83:99:1117,0,1689 -chr6 57466987 rs12205887 T C 1230.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.854;ClippingRankSum=-0.004;DB;DP=98;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.33;MQ0=0;MQRankSum=0.575;QD=12.56;ReadPosRankSum=-0.126;SOR=0.389;VQSLOD=3.29;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:58,40:98:99:1259,0,2007 -chr6 57467084 rs9885913 A G 2211.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=4.628;ClippingRankSum=0.293;DB;DP=304;FS=4.869;MLEAC=1;MLEAF=0.5;MQ=58.78;MQ0=0;MQRankSum=-0.944;NEGATIVE_TRAIN_SITE;QD=7.28;ReadPosRankSum=3.057;SOR=1.014;VQSLOD=-2.572;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:233,71:304:99:2240,0,9850 -chr6 57467093 rs9885916 A G 2301.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=7.069;ClippingRankSum=0.184;DB;DP=312;FS=3.079;MLEAC=1;MLEAF=0.5;MQ=58.58;MQ0=0;MQRankSum=-1.638;NEGATIVE_TRAIN_SITE;QD=7.38;ReadPosRankSum=0.912;SOR=0.918;VQSLOD=-2.342;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:239,73:312:99:2330,0,10451 -chr6 57467100 rs4535533 G C 6947.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-2.106;ClippingRankSum=-2.135;DB;DP=314;FS=1.422;MLEAC=1;MLEAF=0.5;MQ=58.67;MQ0=0;MQRankSum=-0.67;NEGATIVE_TRAIN_SITE;QD=22.13;ReadPosRankSum=0.52;SOR=0.8;VQSLOD=-1.704;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:122,192:314:99:6976,0,3683 -chr6 57467107 rs9885751 C T 1881.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=6.859;ClippingRankSum=-1.729;DB;DP=314;FS=5.484;MLEAC=1;MLEAF=0.5;MQ=58.52;MQ0=0;MQRankSum=-1.808;NEGATIVE_TRAIN_SITE;QD=5.99;ReadPosRankSum=0.287;SOR=1.037;VQSLOD=-2.38;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:238,76:314:99:1910,0,9279 -chr6 57467175 rs4406234 A G 2889.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=2.932;ClippingRankSum=-0.383;DB;DP=258;FS=0.469;MLEAC=1;MLEAF=0.5;MQ=58.12;MQ0=0;MQRankSum=0.153;NEGATIVE_TRAIN_SITE;QD=11.2;ReadPosRankSum=4.087;SOR=0.741;VQSLOD=-0.735;culprit=ReadPosRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:159,99:258:99:2918,0,5132 -chr6 57467279 rs6459263 T C 1140.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=5.633;ClippingRankSum=1.776;DB;DP=140;FS=4.536;MLEAC=1;MLEAF=0.5;MQ=58.17;MQ0=0;MQRankSum=1.542;NEGATIVE_TRAIN_SITE;QD=8.15;ReadPosRankSum=-0.103;SOR=0.269;VQSLOD=-1.496;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:104,36:140:99:1169,0,4245 -chr6 57467282 rs6459264 T C 1140.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.755;ClippingRankSum=1.153;DB;DP=134;FS=1.319;MLEAC=1;MLEAF=0.5;MQ=58.08;MQ0=0;MQRankSum=1.02;POSITIVE_TRAIN_SITE;QD=8.51;ReadPosRankSum=-0.325;SOR=0.374;VQSLOD=1.58;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:100,34:134:99:1169,0,4245 -chr6 57467303 rs1022846 A G 3478.77 PASS AC=2;AF=1.0;AN=2;DB;DP=90;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.39;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.14;SOR=5.33;VQSLOD=6.74;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,90:90:99:3507,271,0 -chr6 57467317 rs4637646 G T 1210.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.996;ClippingRankSum=-0.892;DB;DP=73;FS=4.921;MLEAC=1;MLEAF=0.5;MQ=56.76;MQ0=0;MQRankSum=0.26;QD=16.59;ReadPosRankSum=0.593;SOR=0.14;VQSLOD=0.741;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:40,33:73:99:1239,0,1596 -chr6 57467323 rs4424069 G C 1161.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.993;ClippingRankSum=-0.17;DB;DP=67;FS=4.828;MLEAC=1;MLEAF=0.5;MQ=56.83;MQ0=0;MQRankSum=-0.107;QD=17.34;ReadPosRankSum=0.648;SOR=0.15;VQSLOD=0.857;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:36,31:67:99:1190,0,1431 -chr6 57467456 rs4358625 T G 43.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=14.59;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=1.27;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:31:72,0,31 -chr6 57472201 rs9885694 A G 75.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.054;ClippingRankSum=-0.248;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.573;QD=8.42;ReadPosRankSum=1.683;SOR=0.283;VQSLOD=3.58;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:6,3:9:99:104,0,207 -chr6 57472212 rs9296899 T A 251.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.531;ClippingRankSum=1.531;DB;DP=11;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.377;QD=22.89;ReadPosRankSum=0.382;SOR=1.802;VQSLOD=4.3;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:3,8:11:88:280,0,88 -chr6 57472255 rs9296900 C T 533.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.047;ClippingRankSum=-1.484;DB;DP=20;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=61.07;MQ0=0;MQRankSum=0.524;POSITIVE_TRAIN_SITE;QD=26.69;ReadPosRankSum=-0.786;SOR=2.093;VQSLOD=5.22;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:5,15:20:99:562,0,141 -chr6 57472299 rs9396358 A G 360.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.622;ClippingRankSum=0.811;DB;DP=34;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.59;MQ0=0;MQRankSum=-0.811;QD=10.61;ReadPosRankSum=-1.46;SOR=0.874;VQSLOD=2.75;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:22,12:34:99:389,0,704 -chr6 57472315 rs9296901 A G 1165.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=1.692;ClippingRankSum=-0.988;DB;DP=43;FS=2.613;MLEAC=1;MLEAF=0.5;MQ=58.45;MQ0=0;MQRankSum=0.663;QD=27.11;ReadPosRankSum=-1.151;SOR=0.271;VQSLOD=-0.5021;culprit=ReadPosRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:12,31:43:99:1194,0,341 -chr6 57472316 rs9382818 G A 458.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.993;ClippingRankSum=-0.012;DB;DP=43;FS=2.578;MLEAC=1;MLEAF=0.5;MQ=58.45;MQ0=0;MQRankSum=-0.36;QD=10.67;ReadPosRankSum=-1.95;SOR=0.156;VQSLOD=0.405;culprit=ReadPosRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:26,17:43:99:487,0,974 -chr6 57472344 rs111230027 A AT 305.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.049;ClippingRankSum=0.23;DB;DP=64;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.71;MQ0=0;MQRankSum=1.887;POSITIVE_TRAIN_SITE;QD=4.78;ReadPosRankSum=-0.919;SOR=0.495;VQSLOD=5.04;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:43,17:60:99:343,0,1062 -chr6 57472476 rs9382819 T C 344.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.397;ClippingRankSum=1.197;DB;DP=44;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.95;MQ0=0;MQRankSum=-0.718;QD=7.84;ReadPosRankSum=-1.021;SOR=1.226;VQSLOD=1.17;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:30,14:44:99:373,0,1080 -chr6 57472488 rs9382820 C T 419.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.192;ClippingRankSum=0.268;DB;DP=43;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.92;MQ0=0;MQRankSum=0.395;QD=9.76;ReadPosRankSum=-1.949;SOR=0.836;VQSLOD=2.8;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:28,15:43:99:448,0,1080 -chr6 57472495 rs62400219 C G 263.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.265;ClippingRankSum=-0.448;DB;DP=38;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.78;MQ0=0;MQRankSum=-0.215;QD=6.94;ReadPosRankSum=-0.05;SOR=0.481;VQSLOD=2.66;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:28,10:38:99:292,0,1144 -chr6 57472533 rs9367767 T C 332.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.074;ClippingRankSum=-1.122;DB;DP=17;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.8;MQ0=0;MQRankSum=-0.83;QD=19.57;ReadPosRankSum=0.049;SOR=0.33;VQSLOD=4.65;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:7,10:17:99:361,0,224 -chr6 57472534 rs74369127 T C 46.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=1.197;ClippingRankSum=0.441;DB;DP=17;FS=7.533;MLEAC=1;MLEAF=0.5;MQ=55.8;MQ0=0;MQRankSum=0.189;NEGATIVE_TRAIN_SITE;QD=2.75;ReadPosRankSum=-1.449;SOR=0.01;VQSLOD=-1.589;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:14,3:17:75:75,0,661 -chr6 57474882 rs62400254 A T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.96;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57474896 rs62400255 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.22;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57476586 rs58187447 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57476608 rs57642151 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57479216 rs4530864 T C 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=7.01;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 57482492 rs12197718 T C 39.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=19.87;SOR=2.303;VQSLOD=6.88;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0 -chr6 57483749 rs9476179 C T 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:35:40,0,35 -chr6 57485342 rs9885648 T C 10.2 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.804;ClippingRankSum=0.804;DB;DP=2;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.804;QD=5.1;ReadPosRankSum=0.804;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,1:2:35:38,0,35 -chr6 57485391 rs1853495 T G 15.65 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=15.65;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0 -chr6 57490861 rs11963269 C T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.88;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57490866 rs9885704 C T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.81;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57491118 rs9885817 T C 47.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=15.92;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.98;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:32:76,0,32 -chr6 57492741 rs79386390 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57492762 rs3805807 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57492776 rs77611141 G T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57493700 rs62404095 T G 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.23;SOR=1.609;VQSLOD=6.55;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:6:86,6,0 -chr6 57493709 rs62404096 A G 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=29.37;SOR=2.303;VQSLOD=6.82;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 57493836 rs62404099 C A 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.37;SOR=2.303;VQSLOD=7.43;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 57495024 rs5003525 A C 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=8.86;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 57495215 rs6939623 T G 13.72 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=13.72;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 -chr6 57495238 rs62404102 T C 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=25.87;SOR=0.693;VQSLOD=5.79;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 57497543 rs6929435 C T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.11;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57497562 rs76224813 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.26;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57497579 rs73755610 T G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.63;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57498301 rs11754853 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57498324 rs11759488 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57498894 rs3846934 G A 268.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.827;ClippingRankSum=0.059;DB;DP=15;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.45;MQ0=0;MQRankSum=-0.884;QD=17.92;ReadPosRankSum=-0.177;SOR=1.112;VQSLOD=4.8;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:6,9:15:99:297,0,200 -chr6 57498944 rs3846935 G C 516.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.291;ClippingRankSum=-0.826;DB;DP=30;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.23;MQ0=0;MQRankSum=0.064;QD=17.23;ReadPosRankSum=0.233;SOR=0.784;VQSLOD=4.16;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:12,18:30:99:545,0,370 -chr6 57499042 rs5876654 A AT 87.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.132;ClippingRankSum=-0.57;DB;DP=25;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.51;MQ0=0;MQRankSum=-0.219;POSITIVE_TRAIN_SITE;QD=3.51;ReadPosRankSum=-2.324;SOR=0.77;VQSLOD=4.42;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:13,6:19:99:125,0,294 -chr6 57499171 rs3846936 T C 122.78 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.731;ClippingRankSum=-0.731;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.731;QD=24.56;ReadPosRankSum=-0.731;SOR=1.981;VQSLOD=4.21;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,4:5:25:151,0,25 -chr6 57499188 rs2151627 C T 39.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=13.26;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.9;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:28:68,0,28 -chr6 57499196 rs11423601 C CA 24.75 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=63.51;MQ0=0;MQRankSum=0.736;QD=8.25;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:27:62,0,27 -chr6 57499926 rs2397610 A G 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,2:3:35:40,0,35 -chr6 57500073 rs62404596 G A 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.37;SOR=2.303;VQSLOD=6.89;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 57500104 rs62404597 G A 64.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=63.51;MQ0=0;QD=21.43;SOR=1.179;VQSLOD=6.59;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:92,9,0 -chr6 57500169 rs6926645 T G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.37;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57500181 rs76287706 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=4.49;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57500197 rs11329134 GA G 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.14;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57500204 rs78362714 C T 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57500220 rs4537145 G A 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57500442 rs4540266 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57503123 rs2397930 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57503159 rs3857631 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57503199 rs3996830 T G 35.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=0.0;QD=8.94;ReadPosRankSum=-1.026;SOR=2.303;VQSLOD=4.04;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,2:4:64:64,0,64 -chr6 57503231 rs78058710 A G 140.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;QD=29.11;SOR=1.609;VQSLOD=4.81;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,4:4:12:168,12,0 -chr6 57503398 rs4995671 C A 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.37;SOR=0.693;VQSLOD=7.0;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 57503441 rs4995670 T A 94.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.727;QD=23.69;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.42;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,3:4:33:123,0,33 -chr6 57503444 rs11343070 AC A 85.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.727;POSITIVE_TRAIN_SITE;QD=21.43;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=6.25;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:1,3:4:33:123,0,33 -chr6 57507333 rs148428624 C T 47.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=23.87;SOR=2.303;VQSLOD=6.18;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 57507431 rs139113051 T C 11.83 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=11.83;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0 -chr6 57507846 rs80010809 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57509520 rs62402976 C T 41.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=20.87;SOR=0.693;VQSLOD=6.49;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 -chr6 57511438 rs5011992 G A 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.44;MQ0=0;QD=18.25;SOR=0.693;VQSLOD=6.11;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 57511528 rs10592385 AATAAC A 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.58;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=6.31;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57511564 rs5011994 G A 50.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.58;MQ0=0;QD=25.37;SOR=0.693;VQSLOD=6.78;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 57511607 rs77590924 C T 14.68 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=70.0;MQ0=0;QD=14.68;SOR=1.609;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:41,3,0 -chr6 57511894 rs56224263 T TAC 34.71 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.35;SOR=2.303;VQSLOD=8.87;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 -chr6 57512108 rs6914896 G A 40.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;QD=10.19;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=4.26;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:2,2:4:69:69,0,71 -chr6 57512340 rs4364484 C T 502.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.633;ClippingRankSum=-0.142;DB;DP=25;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.07;MQ0=0;MQRankSum=-1.217;QD=20.11;ReadPosRankSum=-0.311;SOR=1.358;VQSLOD=3.52;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:9,16:25:99:531,0,284 -chr6 57512352 rs5001077 A T 198.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.659;ClippingRankSum=0.512;DB;DP=30;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.23;MQ0=0;MQRankSum=0.415;QD=6.63;ReadPosRankSum=-0.122;SOR=0.155;VQSLOD=2.84;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:21,8:29:99:227,0,724 -chr6 57512439 rs4294006 T C 1438.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=3.959;ClippingRankSum=0.864;DB;DP=144;FS=7.438;MLEAC=1;MLEAF=0.5;MQ=58.55;MQ0=0;MQRankSum=-1.071;QD=9.99;ReadPosRankSum=0.578;SOR=0.083;VQSLOD=-0.7791;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:95,49:144:99:1467,0,3234 -chr6 57512476 rs4307164 G A 5505.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-4.662;ClippingRankSum=2.077;DB;DP=241;FS=1.012;MLEAC=1;MLEAF=0.5;MQ=58.36;MQ0=0;MQRankSum=1.46;NEGATIVE_TRAIN_SITE;QD=22.85;ReadPosRankSum=-2.015;SOR=0.914;VQSLOD=-1.923;culprit=ReadPosRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:78,163:241:99:5534,0,2266 -chr6 57512510 rs4294007 T G 13853.77 PASS AC=2;AF=1.0;AN=2;DB;DP=334;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.18;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.11;SOR=4.194;VQSLOD=3.16;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,334:334:99:13882,1010,0 -chr6 57512529 rs5001076 C A 3081.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-4.175;ClippingRankSum=-2.05;DB;DP=368;FS=3.017;MLEAC=1;MLEAF=0.5;MQ=58.1;MQ0=0;MQRankSum=-0.39;NEGATIVE_TRAIN_SITE;QD=8.37;ReadPosRankSum=0.294;SOR=0.968;VQSLOD=-2.195;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:255,113:368:99:3110,0,8577 -chr6 57512565 rs4294008 T C 9494.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=5.814;ClippingRankSum=0.828;DB;DP=416;FS=5.007;MLEAC=1;MLEAF=0.5;MQ=57.82;MQ0=0;MQRankSum=2.938;NEGATIVE_TRAIN_SITE;QD=22.82;ReadPosRankSum=-0.668;SOR=1.299;VQSLOD=-2.221;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:138,278:416:99:9523,0,3960 -chr6 57512678 rs4398719 G A 11124.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=2.677;ClippingRankSum=0.517;DB;DP=458;FS=4.405;MLEAC=1;MLEAF=0.5;MQ=56.48;MQ0=0;MQRankSum=3.775;NEGATIVE_TRAIN_SITE;QD=24.29;ReadPosRankSum=-0.757;SOR=1.082;VQSLOD=-2.409;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:129,325:454:99:11153,0,3458 -chr6 57512711 rs5001484 G C 5059.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=6.115;ClippingRankSum=-0.961;DB;DP=421;FS=6.509;MLEAC=1;MLEAF=0.5;MQ=53.04;MQ0=0;MQRankSum=1.438;NEGATIVE_TRAIN_SITE;QD=12.02;ReadPosRankSum=0.324;SOR=1.225;VQSLOD=-1.98;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:267,138:405:99:5035,0,6158 -chr6 57512718 rs5001483 T A 4671.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=1.87;ClippingRankSum=0.336;DB;DP=406;FS=3.08;MLEAC=1;MLEAF=0.5;MQ=52.12;MQ0=0;MQRankSum=0.364;NEGATIVE_TRAIN_SITE;QD=11.51;ReadPosRankSum=0.365;SOR=1.044;VQSLOD=-1.109;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:274,131:405:99:4700,0,11219 -chr6 57512740 . CTGTTTT C 1777.73 VQSRTrancheINDEL99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=0.374;ClippingRankSum=0.035;DP=356;FS=2.783;MLEAC=1;MLEAF=0.5;MQ=49.57;MQ0=0;MQRankSum=-7.25;NEGATIVE_TRAIN_SITE;QD=4.99;ReadPosRankSum=-0.198;SOR=0.328;VQSLOD=-3.212;culprit=DP;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:286,64:350:99:1815,0,11798 -chr6 57512775 rs7773110 T G 5490.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-5.254;ClippingRankSum=-0.905;DB;DP=233;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=44.06;MQ0=0;MQRankSum=-4.463;NEGATIVE_TRAIN_SITE;QD=23.57;ReadPosRankSum=-3.464;SOR=1.179;VQSLOD=-2.396;culprit=ReadPosRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:92,138:230:99:5519,0,3342 -chr6 57512779 rs76296076 G T 5369.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-4.88;ClippingRankSum=-0.404;DB;DP=218;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=42.59;MQ0=0;MQRankSum=-5.088;NEGATIVE_TRAIN_SITE;QD=24.63;ReadPosRankSum=-3.913;SOR=1.132;VQSLOD=-2.613;culprit=ReadPosRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:89,129:218:99:5398,0,3366 -chr6 57512787 . T TCACCAAGGC 4709.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=4.158;ClippingRankSum=1.208;DP=186;FS=3.774;MLEAC=1;MLEAF=0.5;MQ=39.95;MQ0=0;MQRankSum=-6.907;QD=25.32;ReadPosRankSum=-2.737;SOR=2.176;VQSLOD=-1.452;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:78,108:186:99:4747,0,3127 -chr6 57512788 . T TTA 4547.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-6.353;ClippingRankSum=-0.603;DP=171;FS=3.354;MLEAC=1;MLEAF=0.5;MQ=40.57;MQ0=0;MQRankSum=-7.416;QD=26.59;ReadPosRankSum=-1.258;SOR=1.878;VQSLOD=-0.9837;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:79,92:171:99:4585,0,3055 -chr6 57512792 rs372064495 T C 3372.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=7.455;ClippingRankSum=-0.198;DB;DP=157;FS=3.151;MLEAC=1;MLEAF=0.5;MQ=40.8;MQ0=0;MQRankSum=-6.089;NEGATIVE_TRAIN_SITE;QD=21.48;ReadPosRankSum=-0.528;SOR=1.733;VQSLOD=-1.961;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:76,81:157:99:3401,0,3097 -chr6 57512793 rs368894562 AATT A 3279.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=7.041;ClippingRankSum=-0.005;DB;DP=158;FS=3.066;MLEAC=1;MLEAF=0.5;MQ=41.17;MQ0=0;MQRankSum=-7.628;QD=20.76;ReadPosRankSum=-0.27;SOR=1.67;VQSLOD=-0.929;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:78,80:158:99:3317,0,3097 -chr6 57512825 rs72880943 C T 1989.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-4.227;ClippingRankSum=-1.068;DB;DP=102;FS=3.096;MLEAC=1;MLEAF=0.5;MQ=44.73;MQ0=0;MQRankSum=-6.811;NEGATIVE_TRAIN_SITE;QD=19.51;ReadPosRankSum=0.098;SOR=1.704;VQSLOD=-2.269;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:50,52:102:99:2018,0,1929 -chr6 57512826 rs7752845 A G 1989.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=6.619;ClippingRankSum=1.207;DB;DP=100;FS=3.098;MLEAC=1;MLEAF=0.5;MQ=45.3;MQ0=0;MQRankSum=-6.799;NEGATIVE_TRAIN_SITE;QD=19.9;ReadPosRankSum=0.336;SOR=1.706;VQSLOD=-2.241;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:49,51:100:99:2018,0,1929 -chr6 57512841 rs78256005 A G 630.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-4.056;ClippingRankSum=-0.094;DB;DP=79;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=46.16;MQ0=0;MQRankSum=-4.822;NEGATIVE_TRAIN_SITE;QD=7.98;ReadPosRankSum=-1.275;SOR=0.455;VQSLOD=-3.272;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:58,21:79:99:659,0,2392 -chr6 57512850 rs77911716 C G 547.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=0.371;ClippingRankSum=-0.636;DB;DP=72;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=46.71;MQ0=0;MQRankSum=-4.402;NEGATIVE_TRAIN_SITE;QD=7.61;ReadPosRankSum=-1.021;SOR=0.357;VQSLOD=-2.865;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:55,17:72:99:576,0,2261 -chr6 57512874 rs71214002 G A 206.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.499;ClippingRankSum=-0.194;DB;DP=49;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=50.3;MQ0=0;MQRankSum=-1.846;QD=4.22;ReadPosRankSum=1.072;SOR=0.058;VQSLOD=0.727;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:40,9:49:99:235,0,1573 -chr6 57512889 rs75351177 C T 149.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-3.464;ClippingRankSum=-0.226;DB;DP=38;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.38;MQ0=0;MQRankSum=-2.862;QD=3.94;ReadPosRankSum=-1.167;SOR=0.061;VQSLOD=-0.8131;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:31,7:38:99:178,0,1252 -chr6 57512893 rs77348569 C T 175.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.044;ClippingRankSum=0.0;DB;DP=34;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=50.45;MQ0=0;MQRankSum=-2.215;QD=5.17;ReadPosRankSum=-0.852;SOR=0.078;VQSLOD=0.483;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:27,7:34:99:204,0,1222 -chr6 57512902 rs77563921 G A 112.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.759;ClippingRankSum=0.9;DB;DP=28;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.17;MQ0=0;MQRankSum=-1.86;QD=4.03;ReadPosRankSum=-1.14;SOR=0.061;VQSLOD=0.509;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:23,5:28:99:141,0,951 -chr6 57512903 rs75209982 C A 112.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-2.939;ClippingRankSum=-1.56;DB;DP=28;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.17;MQ0=0;MQRankSum=-2.939;QD=4.03;ReadPosRankSum=-1.5;SOR=0.061;VQSLOD=-0.8813;culprit=QD;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:23,5:28:99:141,0,951 -chr6 57512906 rs77519815 T A 337.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=0.628;ClippingRankSum=1.732;DB;DP=27;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=48.72;MQ0=0;MQRankSum=-3.289;QD=12.51;ReadPosRankSum=-2.536;SOR=0.317;VQSLOD=-0.8036;culprit=MQRankSum;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:17,10:27:99:366,0,726 -chr6 57512916 rs140176282 A AT 70.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.765;ClippingRankSum=-0.191;DB;DP=22;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.71;MQ0=0;MQRankSum=-1.244;QD=3.22;ReadPosRankSum=-0.67;SOR=0.039;VQSLOD=4.77;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 0/1:19,3:22:99:108,0,828 -chr6 57513042 rs76730673 C T 87.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.77;MQ0=0;QD=29.09;SOR=1.179;VQSLOD=6.6;culprit=FS;GENE=PRIM2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:115,9,0 -chr6 57514007 rs4712214 A G 66.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=22.09;SOR=1.179;VQSLOD=7.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:94,9,0 -chr6 57514048 rs79485395 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57517722 rs75802839 C T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=40.87;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.43;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57517733 rs80270590 T A 96.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=48.1;MQ0=0;QD=32.09;SOR=2.833;VQSLOD=6.48;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:124,9,0 -chr6 57517777 rs76191741 A G 19.81 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=47.71;MQ0=0;MQRankSum=1.026;QD=3.96;ReadPosRankSum=0.0;SOR=0.693 GT:AD:DP:GQ:PL 0/1:2,2:4:37:48,0,37 -chr6 57517837 rs79522959 C T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.28;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57517838 rs1853506 A G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.0;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57517853 rs76412158 A T 10.9 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.9;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:37,3,0 -chr6 57518157 rs4993255 T C 62.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.95;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 57519294 rs5017411 C G 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.17;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57519302 rs79076980 T C 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57519303 rs74656916 A G 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57519820 rs7744217 T C 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.63;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57521340 rs73755643 C G 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57521352 rs74795344 A C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.08;SOR=1.609;VQSLOD=6.03;culprit=FS GT:AD:DP:GQ:PL 1/1:0,1:1:6:90,6,0 -chr6 57521365 rs76281818 G T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.15;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57521370 rs61198018 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.32;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57522688 rs76632457 T C 24.78 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=8.26;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:53,0,33 -chr6 57522722 rs80202467 G T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57522729 rs76599881 G A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=5.83;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57522740 rs78027687 C T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=5.91;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57522743 rs72880950 G A 52.78 PASS AC=1;AF=0.5;AN=2;DB;DP=2;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=29.0;MQ0=0;QD=26.39;SOR=0.693;VQSLOD=7.37;culprit=FS GT:AD:DP:GQ:PL 0/1:0,2:2:26:81,0,26 -chr6 57522745 rs79247610 A C 52.78 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=3.84;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:26:81,0,26 -chr6 57526215 rs5019459 T C 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57526220 rs5019458 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.27;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57526231 rs5019457 A G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.03;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57526585 rs62405765 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.18;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57526610 rs4370353 C T 52.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.16;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 -chr6 57527149 rs77487282 A C 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=27.37;SOR=0.693;VQSLOD=7.86;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 57528643 rs4989228 G A 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:34:40,0,34 -chr6 57529061 rs4580853 C T 46.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=23.37;SOR=0.693;VQSLOD=7.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:74,6,0 -chr6 57529121 rs4236160 A C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57531762 rs2894929 A C 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=45.96;MQ0=0;QD=6.2;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57531763 rs4537146 G A 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=45.96;MQ0=0;QD=6.2;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57536087 rs77762742 T G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57536105 rs77828016 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57538839 rs78941520 C T 43.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=14.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.6;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:32:72,0,32 -chr6 57538866 rs80259399 C T 49.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=0.0;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;QD=12.44;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=4.77;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,118 -chr6 57538867 rs75525472 A G 49.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;QD=12.44;ReadPosRankSum=0.0;SOR=0.693;VQSLOD=4.75;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,118 -chr6 57538878 rs62405823 G A 86.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=-0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.727;QD=21.69;ReadPosRankSum=-0.727;SOR=0.916;VQSLOD=4.39;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:29:115,0,29 -chr6 57539231 rs73753049 C T 11.12 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.804;ClippingRankSum=0.804;DB;DP=2;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.804;QD=5.56;ReadPosRankSum=0.804;SOR=1.447 GT:AD:DP:GQ:PL 0/1:1,1:2:34:39,0,34 -chr6 57539244 rs77110690 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.36;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57539245 rs150830310 G A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.83;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57539260 rs73753050 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57539457 rs62405831 G T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.69;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57539460 rs35133381 AT A 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=8.63;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57539480 rs2498202 T A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=6.95;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57544039 rs2498209 C G 60.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=20.09;SOR=1.179;VQSLOD=7.23;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:88,9,0 -chr6 57546228 rs12212539 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.61;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57546230 rs77288943 G A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.02;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57546234 rs12205399 C T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.35;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57546244 rs79029147 C G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.4;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57546251 rs78287808 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=32.99;SOR=1.609;VQSLOD=6.28;culprit=FS GT:AD:DP:GQ:PL 1/1:0,1:1:6:90,6,0 -chr6 57546252 rs74936228 G A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=30.52;SOR=1.609;VQSLOD=6.97;culprit=FS GT:AD:DP:GQ:PL 1/1:0,1:1:6:90,6,0 -chr6 57546590 rs1853496 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57547418 rs76051348 C T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57547428 rs76625067 C G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.04;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57549247 rs2476489 C G 16.63 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=16.63;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:43,3,0 -chr6 57550746 rs74923423 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57550797 rs78408847 G T 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.18;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 -chr6 57556582 rs2397904 C T 14.68 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=14.68;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:41,3,0 -chr6 57556703 rs2397905 G T 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.37;SOR=0.693;VQSLOD=7.3;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 57556977 rs113627621 T C 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.35;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57556995 rs113330746 A G 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57557004 rs4425585 C T 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57560942 rs3903831 C G 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57560949 rs4097974 T C 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57562969 rs77727649 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57564830 rs78356131 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.07;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57564831 rs77336271 G A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.64;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57564861 rs6932761 T C 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=6.77;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 57565509 rs11965356 T G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57570509 rs78347797 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57570530 rs6903247 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57574113 rs5008152 G A 71.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 -chr6 57574138 rs5008153 T A 61.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=20.43;SOR=1.179;VQSLOD=6.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 -chr6 57576825 rs73755103 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57576836 rs73755104 T G 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57576845 rs73755105 C G 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57595707 rs72871580 T C 52.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=4.61;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 -chr6 57595709 rs72871582 C T 52.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.48;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 -chr6 57595723 rs75919230 C G 83.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.727;ClippingRankSum=-0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=0.727;QD=20.94;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.77;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:33:112,0,33 -chr6 57595732 rs72871584 G T 83.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=0.727;QD=20.94;ReadPosRankSum=-0.727;SOR=0.916;VQSLOD=4.48;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:33:112,0,33 -chr6 57595770 rs73756249 A G 34.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=0.0;QD=8.69;ReadPosRankSum=1.026;SOR=2.303;VQSLOD=4.24;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:37:63,0,37 -chr6 57595781 rs73457550 G A 33.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=0.0;QD=8.44;ReadPosRankSum=1.026;SOR=2.303;VQSLOD=3.9;culprit=QD GT:AD:DP:GQ:PL 0/1:2,2:4:37:62,0,37 -chr6 57595820 rs73756251 T G 76.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=0.727;QD=19.19;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.66;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:29:105,0,29 -chr6 57595832 rs77557182 T C 11.12 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.804;ClippingRankSum=0.804;DB;DP=2;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.804;QD=5.56;ReadPosRankSum=0.804;SOR=1.447 GT:AD:DP:GQ:PL 0/1:1,1:2:39:39,0,39 -chr6 57595845 rs76008427 A T 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57597257 rs72871594 A T 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=25.87;SOR=0.693;VQSLOD=7.04;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 57597260 rs72871595 A T 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=30.27;SOR=1.609;VQSLOD=6.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,1:1:6:79,6,0 -chr6 57603832 rs80257130 A T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.47;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57603839 rs147344208 A AT 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=5.92;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57603845 rs72873407 C T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.34;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57606933 rs73757604 T C 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.37;SOR=2.303;VQSLOD=7.85;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 57606965 rs74644238 T G 66.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=22.09;SOR=1.179;VQSLOD=6.18;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:94,9,0 -chr6 57606996 rs73459287 G C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57607035 rs73757606 G C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.07;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57607044 rs73757607 A G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.28;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57607068 rs72873457 C T 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57607074 rs4360139 G C 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57608079 rs73459299 A C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57612661 . G A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57618295 rs5876690 G GA 25.72 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=12.86;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:62,6,0 -chr6 57673397 rs7765475 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57686962 rs140945786 G T 100.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.754;ClippingRankSum=1.754;DB;DP=7;FS=15.441;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.55;POSITIVE_TRAIN_SITE;QD=14.4;ReadPosRankSum=0.937;SOR=3.221;VQSLOD=0.651;culprit=FS;GENE=GAPDHP41 GT:AD:DP:GQ:PL 0/1:3,4:7:99:129,0,102 -chr6 57699097 rs6459305 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57710858 rs149357140 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57711844 rs143767848 A T 49.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=8.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 57723952 rs11295509 CA C 37.25 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=12.42;SOR=1.179;VQSLOD=5.67;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:74,9,0 -chr6 57732063 . C A 12.13 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=3.03;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:17:40,0,17 -chr6 57737999 rs142093663 G A 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=27.87;SOR=0.693;VQSLOD=6.23;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 57738613 . C T 20.78 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.39;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:48,6,0 -chr6 57785184 rs116169256 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57826827 . TA T 24.72 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.24;MQ0=0;QD=12.36;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 -chr6 57841273 rs188364530 C T 1364.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.628;ClippingRankSum=0.296;DB;DP=85;FS=7.134;MLEAC=1;MLEAF=0.5;MQ=59.34;MQ0=0;MQRankSum=1.622;POSITIVE_TRAIN_SITE;QD=16.06;ReadPosRankSum=-0.11;SOR=0.843;VQSLOD=1.24;culprit=FS;GENE=RBBP4P3 GT:AD:DP:GQ:PL 0/1:38,47:85:99:1393,0,1205 -chr6 57841320 rs140816261 G T 1315.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.878;ClippingRankSum=-0.287;DB;DP=83;FS=5.67;MLEAC=1;MLEAF=0.5;MQ=57.34;MQ0=0;MQRankSum=-0.132;POSITIVE_TRAIN_SITE;QD=15.85;ReadPosRankSum=-0.515;SOR=1.312;VQSLOD=1.62;culprit=FS;GENE=RBBP4P3 GT:AD:DP:GQ:PL 0/1:40,43:83:99:1344,0,1358 -chr6 57841627 rs149540211 AC A 954.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.085;ClippingRankSum=0.306;DB;DP=80;FS=3.046;MLEAC=1;MLEAF=0.5;MQ=59.31;MQ0=0;MQRankSum=1.819;QD=11.93;ReadPosRankSum=-1.129;SOR=0.798;VQSLOD=0.74;culprit=MQRankSum;GENE=RBBP4P3 GT:AD:DP:GQ:PL 0/1:42,36:78:99:992,0,1172 -chr6 57842518 rs149985050 G T 70.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.754;ClippingRankSum=0.0;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=10.11;ReadPosRankSum=0.937;SOR=0.495;VQSLOD=5.83;culprit=FS;GENE=RBBP4P3 GT:AD:DP:GQ:PL 0/1:4,3:7:99:99,0,144 -chr6 57843574 rs115026909 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57857856 rs3000344 T C 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=45.19;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.46;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57972306 rs55752203 TG T 24.72 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.84;MQ0=0;QD=12.36;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 -chr6 57977600 rs115553313 C T 97.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.43;SOR=1.179;VQSLOD=8.27;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:125,9,0 -chr6 57977640 rs4960490 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57998262 rs9476413 T C 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=6.67;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 58028492 rs147632909 C A 37.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=0.0;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=9.44;ReadPosRankSum=0.0;SOR=2.303;VQSLOD=5.34;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:66:66,0,74 -chr6 58039789 rs9382925 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 58165037 . T G 62.74 PASS AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.84;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 58165039 . A G 62.74 PASS AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.45;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 58165065 . GT G 53.7 PASS AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=5.77;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 58173632 rs114670858 T G 20.78 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=10.39;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:48,6,0 -chr6 58246055 rs6918567 T C 2357.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.591;ClippingRankSum=-0.427;DB;DP=249;FS=6.315;MLEAC=1;MLEAF=0.5;MQ=50.51;MQ0=0;MQRankSum=-11.921;POSITIVE_TRAIN_SITE;QD=9.47;ReadPosRankSum=2.161;SOR=1.112;VQSLOD=-3.174;culprit=MQRankSum;GENE=GUSBP4 GT:AD:DP:GQ:PL 0/1:179,69:248:99:2386,0,8176 -chr6 58246056 rs6930828 G A 2357.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-3.659;ClippingRankSum=0.056;DB;DP=250;FS=5.251;MLEAC=1;MLEAF=0.5;MQ=50.59;MQ0=0;MQRankSum=-11.878;QD=9.43;ReadPosRankSum=-0.007;SOR=1.079;VQSLOD=-4.553;culprit=MQRankSum;GENE=GUSBP4 GT:AD:DP:GQ:PL 0/1:179,70:249:99:2386,0,8176 -chr6 58246143 rs6931014 G A 3997.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.856;ClippingRankSum=-0.73;DB;DP=326;FS=0.849;MLEAC=1;MLEAF=0.5;MQ=49.42;MQ0=0;MQRankSum=-4.926;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=12.26;ReadPosRankSum=3.641;SOR=0.631;VQSLOD=-1.659;culprit=MQRankSum;GENE=GUSBP4 GT:AD:DP:GQ:PL 0/1:186,138:324:99:4026,0,5840 -chr6 58250570 rs9500243 A T 402.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.537;ClippingRankSum=0.754;DB;DP=40;FS=8.709;MLEAC=1;MLEAF=0.5;MQ=50.1;MQ0=0;MQRankSum=0.698;POSITIVE_TRAIN_SITE;QD=10.07;ReadPosRankSum=0.112;SOR=0.032;VQSLOD=1.36;culprit=FS;GENE=GUSBP4 GT:AD:DP:GQ:PL 0/1:25,15:40:99:431,0,789 -chr6 58252949 . A G 37.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.322;ClippingRankSum=-0.684;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=36.3;MQ0=0;MQRankSum=-0.684;QD=4.72;ReadPosRankSum=0.322;SOR=0.368;VQSLOD=3.52;culprit=QD;GENE=GUSBP4 GT:AD:DP:GQ:PL 0/1:5,3:8:66:66,0,144 -chr6 58260059 rs74657950 G A 177.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.067;ClippingRankSum=0.058;DB;DP=15;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.79;MQ0=0;MQRankSum=-2.025;QD=11.85;ReadPosRankSum=0.984;SOR=0.582;VQSLOD=2.97;culprit=FS;GENE=GUSBP4 GT:AD:DP:GQ:PL 0/1:8,7:15:99:206,0,240 -chr6 58260138 rs62464086 A G 246.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.547;ClippingRankSum=-0.921;DB;DP=43;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.77;MQ0=0;MQRankSum=-2.308;QD=5.74;ReadPosRankSum=0.921;SOR=0.569;VQSLOD=0.439;culprit=QD;GENE=GUSBP4 GT:AD:DP:GQ:PL 0/1:28,14:42:99:275,0,785 -chr6 58263609 rs4079740 A G 17.84 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=1.231;ClippingRankSum=-1.231;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=44.65;MQ0=0;MQRankSum=-1.231;QD=3.57;ReadPosRankSum=0.358;SOR=0.446;GENE=GUSBP4,POM121L14P GT:AD:DP:GQ:PL 0/1:3,2:5:46:46,0,99 -chr6 58263871 rs6588681 T C 325.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.892;ClippingRankSum=-0.055;DB;DP=33;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=52.21;MQ0=0;MQRankSum=-2.022;QD=9.87;ReadPosRankSum=1.73;SOR=0.941;VQSLOD=1.68;culprit=FS;GENE=POM121L14P GT:AD:DP:GQ:PL 0/1:19,14:33:99:354,0,577 -chr6 58263932 rs1810425 G A 548.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.642;ClippingRankSum=-0.644;DB;DP=42;FS=1.298;MLEAC=1;MLEAF=0.5;MQ=56.18;MQ0=0;MQRankSum=-0.407;QD=13.07;ReadPosRankSum=-0.223;SOR=1.002;VQSLOD=1.43;culprit=FS;GENE=POM121L14P GT:AD:DP:GQ:PL 0/1:23,18:41:99:577,0,758 -chr6 58263952 rs1810426 A G 478.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.162;ClippingRankSum=-0.058;DB;DP=46;FS=2.893;MLEAC=1;MLEAF=0.5;MQ=56.38;MQ0=0;MQRankSum=1.471;QD=10.41;ReadPosRankSum=0.683;SOR=1.251;VQSLOD=1.23;culprit=QD;GENE=POM121L14P GT:AD:DP:GQ:PL 0/1:27,18:45:99:507,0,927 -chr6 58265128 rs9391382 T C 346.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=1.844;ClippingRankSum=-0.596;DB;DP=54;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=43.99;MQ0=0;MQRankSum=-5.275;NEGATIVE_TRAIN_SITE;QD=6.42;ReadPosRankSum=-1.037;SOR=0.793;VQSLOD=-3.62;culprit=MQRankSum;GENE=POM121L14P GT:AD:DP:GQ:PL 0/1:36,18:54:99:375,0,1179 -chr6 58265398 rs17488291 G A 1245.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.662;ClippingRankSum=0.505;DB;DP=89;FS=7.385;MLEAC=1;MLEAF=0.5;MQ=53.47;MQ0=0;MQRankSum=-1.229;POSITIVE_TRAIN_SITE;QD=14.0;ReadPosRankSum=1.648;SOR=1.478;VQSLOD=1.83;culprit=FS;GENE=POM121L14P GT:AD:DP:GQ:PL 0/1:47,42:89:99:1274,0,1450 -chr6 58265469 . G GTTT 400.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.047;ClippingRankSum=1.203;DP=68;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=52.92;MQ0=0;MQRankSum=-3.451;QD=5.89;ReadPosRankSum=-0.359;SOR=0.651;VQSLOD=1.97;culprit=FS;GENE=POM121L14P GT:AD:DP:GQ:PL 0/1:34,19:53:99:438,0,1230 -chr6 58273526 rs4928423 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.0;MQ0=0;QD=10.88;SOR=0.693;GENE=LINC00680 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 58287821 rs9404620 A G 128.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.307;ClippingRankSum=0.876;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.39;MQ0=0;MQRankSum=0.729;POSITIVE_TRAIN_SITE;QD=14.31;ReadPosRankSum=0.0;SOR=0.892;VQSLOD=6.42;culprit=FS;GENE=LINC00680 GT:AD:DP:GQ:PL 0/1:4,5:9:99:157,0,118 -chr6 58294828 rs2012049 C T 129.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.663;ClippingRankSum=-0.251;DB;DP=17;FS=2.884;MLEAC=1;MLEAF=0.5;MQ=51.67;MQ0=0;MQRankSum=-2.161;POSITIVE_TRAIN_SITE;QD=7.63;ReadPosRankSum=-0.151;SOR=1.688;VQSLOD=0.937;culprit=QD;GENE=GAPDHP15 GT:AD:DP:GQ:PL 0/1:11,6:17:99:158,0,414 -chr6 58302194 rs693484 T A 47.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=0.693;VQSLOD=8.67;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 58365506 rs60186309 T TA 41.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.85;SOR=0.693;VQSLOD=8.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 58447068 rs1224740 A G 1017.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.8;ClippingRankSum=-0.222;DB;DP=64;FS=3.511;MLEAC=1;MLEAF=0.5;MQ=58.23;MQ0=0;MQRankSum=0.316;POSITIVE_TRAIN_SITE;QD=15.9;ReadPosRankSum=-0.356;SOR=1.296;VQSLOD=3.1;culprit=ReadPosRankSum;GENE=RBBP4P4 GT:AD:DP:GQ:PL 0/1:32,32:64:99:1046,0,1021 -chr6 58465552 rs1224802 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=22.51;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 58490384 rs7770844 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 58693830 rs2343003 A C 60.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=2.303;VQSLOD=9.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:88,6,0 -chr6 58735978 rs2343014 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 58776289 rs4357163 T G 186.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=2.202;ClippingRankSum=0.775;DB;DP=26;FS=2.192;MLEAC=1;MLEAF=0.5;MQ=33.3;MQ0=0;MQRankSum=-1.085;QD=7.18;ReadPosRankSum=0.837;SOR=1.46;VQSLOD=0.168;culprit=QD GT:AD:DP:GQ:PL 0/1:13,10:23:99:215,0,418 -chr6 58776318 rs9986349 A G 261.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.368;ClippingRankSum=-0.152;DB;DP=22;FS=2.098;MLEAC=1;MLEAF=0.5;MQ=32.68;MQ0=0;MQRankSum=-0.684;QD=11.9;ReadPosRankSum=-0.304;SOR=0.243;VQSLOD=1.18;culprit=QD GT:AD:DP:GQ:PL 0/1:11,9:20:99:290,0,435 -chr6 58776319 rs9638012 C T 871.77 PASS AC=2;AF=1.0;AN=2;DB;DP=22;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=32.68;MQ0=0;QD=28.76;SOR=2.093;VQSLOD=5.62;culprit=FS GT:AD:DP:GQ:PL 1/1:0,20:20:60:900,60,0 -chr6 58776352 rs4317432 T C 267.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.799;ClippingRankSum=-0.318;DB;DP=17;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=32.04;MQ0=0;MQRankSum=-0.847;QD=15.75;ReadPosRankSum=-1.059;SOR=0.653;VQSLOD=4.28;culprit=FS GT:AD:DP:GQ:PL 0/1:7,9:16:99:296,0,314 -chr6 58776411 rs9638013 A G 364.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.887;ClippingRankSum=-1.415;DB;DP=18;FS=2.846;MLEAC=1;MLEAF=0.5;MQ=28.44;MQ0=0;MQRankSum=-0.283;QD=20.26;ReadPosRankSum=0.962;SOR=0.148;VQSLOD=1.19;culprit=QD GT:AD:DP:GQ:PL 0/1:4,13:17:99:393,0,132 -chr6 58776442 rs9638019 T C 491.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.786;ClippingRankSum=0.381;DB;DP=25;FS=2.593;MLEAC=1;MLEAF=0.5;MQ=35.87;MQ0=0;MQRankSum=-0.498;QD=19.67;ReadPosRankSum=0.088;SOR=1.863;VQSLOD=1.35;culprit=QD GT:AD:DP:GQ:PL 0/1:10,14:24:99:520,0,292 -chr6 58776542 rs4524636 G A 45.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=0.367;ClippingRankSum=0.115;DB;DP=64;FS=1.496;MLEAC=1;MLEAF=0.5;MQ=48.96;MQ0=0;MQRankSum=0.136;NEGATIVE_TRAIN_SITE;QD=0.72;ReadPosRankSum=-0.073;SOR=1.179;VQSLOD=-1.126;culprit=QD GT:AD:DP:GQ:PL 0/1:54,8:62:74:74,0,1805 -chr6 58776555 rs4928523 T C 742.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.227;ClippingRankSum=-0.403;DB;DP=63;FS=9.224;MLEAC=1;MLEAF=0.5;MQ=49.77;MQ0=0;MQRankSum=0.433;QD=11.79;ReadPosRankSum=1.884;SOR=1.229;VQSLOD=0.004;culprit=FS GT:AD:DP:GQ:PL 0/1:36,25:61:99:771,0,1202 -chr6 58776592 rs9377908 A G 222.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-3.65;ClippingRankSum=-0.434;DB;DP=74;FS=1.153;MLEAC=1;MLEAF=0.5;MQ=54.28;MQ0=0;MQRankSum=0.889;NEGATIVE_TRAIN_SITE;QD=3.01;ReadPosRankSum=0.918;SOR=0.46;VQSLOD=-0.9187;culprit=QD GT:AD:DP:GQ:PL 0/1:58,14:72:99:251,0,2116 -chr6 58776745 rs9632507 C T 3168.77 PASS AC=2;AF=1.0;AN=2;DB;DP=80;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=55.29;MQ0=0;QD=32.18;SOR=0.927;VQSLOD=5.45;culprit=FS GT:AD:DP:GQ:PL 1/1:0,74:74:99:3197,226,0 -chr6 58776782 rs9632508 A T 3215.77 PASS AC=2;AF=1.0;AN=2;DB;DP=83;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=54.76;MQ0=0;QD=30.1;SOR=0.887;VQSLOD=5.64;culprit=FS GT:AD:DP:GQ:PL 1/1:0,77:77:99:3244,240,0 -chr6 58776802 rs4401693 T G 670.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.16;ClippingRankSum=-0.171;DB;DP=80;FS=3.349;MLEAC=1;MLEAF=0.5;MQ=54.82;MQ0=0;MQRankSum=2.069;QD=8.38;ReadPosRankSum=0.137;SOR=1.112;VQSLOD=-0.5951;culprit=QD GT:AD:DP:GQ:PL 0/1:49,25:74:99:699,0,1658 -chr6 58776855 rs4928552 A G 1233.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.182;ClippingRankSum=0.37;DB;DP=79;FS=1.923;MLEAC=1;MLEAF=0.5;MQ=54.95;MQ0=0;MQRankSum=1.187;QD=15.62;ReadPosRankSum=-0.469;SOR=0.872;VQSLOD=1.36;culprit=DP GT:AD:DP:GQ:PL 0/1:35,38:73:99:1262,0,1231 -chr6 58776887 rs113904338 A G 105.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=3.374;ClippingRankSum=-1.479;DB;DP=74;FS=1.493;MLEAC=1;MLEAF=0.5;MQ=54.73;MQ0=0;MQRankSum=1.286;NEGATIVE_TRAIN_SITE;QD=1.43;ReadPosRankSum=1.305;SOR=1.159;VQSLOD=-1.368;culprit=QD GT:AD:DP:GQ:PL 0/1:59,8:67:99:134,0,2069 -chr6 58776958 rs4562168 A T 38.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.772;ClippingRankSum=1.153;DB;DP=68;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.56;MQ0=0;MQRankSum=0.582;QD=0.57;ReadPosRankSum=1.725;SOR=0.941;VQSLOD=0.88;culprit=QD GT:AD:DP:GQ:PL 0/1:58,7:65:67:67,0,2198 -chr6 58776965 rs9632509 C T 18.82 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.964;ClippingRankSum=-1.381;DB;DP=72;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=52.35;MQ0=0;MQRankSum=1.202;QD=0.26;ReadPosRankSum=1.441;SOR=0.796 GT:AD:DP:GQ:PL 0/1:62,7:69:47:47,0,2234 -chr6 58776982 rs9632510 G T 1497.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-3.267;ClippingRankSum=0.065;DB;DP=67;FS=1.041;MLEAC=1;MLEAF=0.5;MQ=51.72;MQ0=0;MQRankSum=-0.411;QD=22.35;ReadPosRankSum=-0.887;SOR=0.51;VQSLOD=-0.2878;culprit=FS GT:AD:DP:GQ:PL 0/1:19,46:65:99:1526,0,547 -chr6 58776984 rs56092323 A T 39.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.0;ClippingRankSum=0.603;DB;DP=67;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=51.72;MQ0=0;MQRankSum=1.386;QD=0.59;ReadPosRankSum=1.323;SOR=0.787;VQSLOD=0.978;culprit=QD GT:AD:DP:GQ:PL 0/1:58,7:65:68:68,0,2352 -chr6 58777039 rs28781680 G A 376.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.782;ClippingRankSum=-0.924;DB;DP=63;FS=4.123;MLEAC=1;MLEAF=0.5;MQ=46.06;MQ0=0;MQRankSum=1.682;QD=5.98;ReadPosRankSum=-0.766;SOR=1.179;VQSLOD=-0.5013;culprit=QD GT:AD:DP:GQ:PL 0/1:47,16:63:99:405,0,1853 -chr6 58777056 rs9654654 G T 772.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-1.293;ClippingRankSum=0.839;DB;DP=64;FS=5.15;MLEAC=1;MLEAF=0.5;MQ=45.93;MQ0=0;MQRankSum=1.899;QD=12.07;ReadPosRankSum=-0.041;SOR=1.004;VQSLOD=0.153;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:39,25:64:99:801,0,1404 -chr6 58777074 rs4388312 C T 822.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.624;ClippingRankSum=-1.281;DB;DP=65;FS=6.614;MLEAC=1;MLEAF=0.5;MQ=49.69;MQ0=0;MQRankSum=0.164;QD=12.66;ReadPosRankSum=-1.018;SOR=0.612;VQSLOD=0.293;culprit=FS GT:AD:DP:GQ:PL 0/1:34,31:65:99:851,0,1154 -chr6 58777106 rs4610595 A G 643.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=0.791;ClippingRankSum=1.422;DB;DP=67;FS=5.024;MLEAC=1;MLEAF=0.5;MQ=56.66;MQ0=0;MQRankSum=-0.611;QD=9.61;ReadPosRankSum=0.573;SOR=0.565;VQSLOD=0.035;culprit=QD GT:AD:DP:GQ:PL 0/1:41,26:67:99:672,0,1465 -chr6 58777109 rs9647639 C T 510.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-2.158;ClippingRankSum=0.783;DB;DP=69;FS=9.064;MLEAC=1;MLEAF=0.5;MQ=57.11;MQ0=0;MQRankSum=0.783;NEGATIVE_TRAIN_SITE;QD=7.4;ReadPosRankSum=-1.203;SOR=1.679;VQSLOD=-1.89;culprit=QD GT:AD:DP:GQ:PL 0/1:46,23:69:99:539,0,1603 -chr6 58777156 rs4577825 C G 121.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.79;ClippingRankSum=0.33;DB;DP=81;FS=4.661;MLEAC=1;MLEAF=0.5;MQ=57.6;MQ0=0;MQRankSum=1.12;NEGATIVE_TRAIN_SITE;QD=1.5;ReadPosRankSum=-0.258;SOR=1.196;VQSLOD=-2.068;culprit=QD GT:AD:DP:GQ:PL 0/1:67,11:78:99:150,0,2400 -chr6 58777178 rs9638022 G T 2960.77 PASS AC=2;AF=1.0;AN=2;DB;DP=78;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.64;MQ0=0;QD=28.06;SOR=0.774;VQSLOD=5.1;culprit=FS GT:AD:DP:GQ:PL 1/1:0,75:75:99:2989,229,0 -chr6 58777233 rs4336468 C T 554.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.43;ClippingRankSum=-1.64;DB;DP=65;FS=1.047;MLEAC=1;MLEAF=0.5;MQ=57.82;MQ0=0;MQRankSum=0.052;QD=8.53;ReadPosRankSum=0.696;SOR=0.914;VQSLOD=0.514;culprit=QD GT:AD:DP:GQ:PL 0/1:44,19:63:99:583,0,1593 -chr6 58777237 rs4518527 A G 633.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-4.144;ClippingRankSum=0.639;DB;DP=59;FS=5.406;MLEAC=1;MLEAF=0.5;MQ=58.17;MQ0=0;MQRankSum=1.634;QD=10.74;ReadPosRankSum=-0.971;SOR=0.569;VQSLOD=-0.0454;culprit=QD GT:AD:DP:GQ:PL 0/1:34,24:58:99:662,0,1277 -chr6 58777276 rs4446588 A C 897.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.1;ClippingRankSum=0.236;DB;DP=62;FS=0.99;MLEAC=1;MLEAF=0.5;MQ=57.73;MQ0=0;MQRankSum=1.879;QD=14.48;ReadPosRankSum=0.023;SOR=0.662;VQSLOD=0.954;culprit=FS GT:AD:DP:GQ:PL 0/1:32,27:59:99:926,0,946 -chr6 58777295 rs9638023 T C 2798.77 PASS AC=2;AF=1.0;AN=2;DB;DP=67;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.73;MQ0=0;QD=33.48;SOR=0.79;VQSLOD=5.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,63:63:99:2827,196,0 -chr6 58777312 rs9632511 T C 759.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=0.614;ClippingRankSum=-1.05;DB;DP=72;FS=11.531;MLEAC=1;MLEAF=0.5;MQ=57.36;MQ0=0;MQRankSum=-1.776;QD=10.55;ReadPosRankSum=0.984;SOR=1.631;VQSLOD=-1.664;culprit=FS GT:AD:DP:GQ:PL 0/1:44,23:67:99:788,0,1478 -chr6 58777366 rs9632513 A G 2731.77 PASS AC=2;AF=1.0;AN=2;DB;DP=68;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.45;MQ0=0;QD=29.84;SOR=0.756;VQSLOD=5.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,64:64:99:2760,199,0 -chr6 58777546 rs9632515 G A 2432.77 PASS AC=2;AF=1.0;AN=2;DB;DP=69;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.61;MQ0=0;QD=30.91;SOR=0.723;VQSLOD=5.57;culprit=FS GT:AD:DP:GQ:PL 1/1:0,67:67:99:2461,201,0 -chr6 58777573 rs9632516 C T 2295.77 VQSRTrancheSNP99.00to99.90 AC=2;AF=1.0;AN=2;BaseQRankSum=-0.251;ClippingRankSum=1.138;DB;DP=66;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.3;MQ0=0;MQRankSum=-0.559;NEGATIVE_TRAIN_SITE;QD=34.78;ReadPosRankSum=1.794;SOR=0.826;VQSLOD=-0.6277;culprit=QD GT:AD:DP:GQ:PL 1/1:2,62:64:99:2324,117,0 -chr6 58777583 rs4351287 A G 250.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=2.157;ClippingRankSum=0.238;DB;DP=69;FS=1.199;MLEAC=1;MLEAF=0.5;MQ=55.52;MQ0=0;MQRankSum=-0.221;QD=3.63;ReadPosRankSum=0.648;SOR=0.717;VQSLOD=-0.7794;culprit=QD GT:AD:DP:GQ:PL 0/1:52,13:65:99:279,0,1731 -chr6 58777599 . T G 144.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=0.474;ClippingRankSum=-0.957;DP=71;FS=5.022;MLEAC=1;MLEAF=0.5;MQ=57.05;MQ0=0;MQRankSum=-0.563;NEGATIVE_TRAIN_SITE;QD=2.04;ReadPosRankSum=-0.063;SOR=0.899;VQSLOD=-1.822;culprit=QD GT:AD:DP:GQ:PL 0/1:56,10:66:99:173,0,1929 -chr6 58777775 . A C 471.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=0.3;ClippingRankSum=0.625;DP=64;FS=1.059;MLEAC=1;MLEAF=0.5;MQ=56.1;MQ0=0;MQRankSum=0.17;QD=7.37;ReadPosRankSum=1.517;SOR=0.904;VQSLOD=0.168;culprit=QD GT:AD:DP:GQ:PL 0/1:40,19:59:99:500,0,1465 -chr6 58777789 rs4296911 T C 850.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=1.376;ClippingRankSum=-0.201;DB;DP=67;FS=8.737;MLEAC=1;MLEAF=0.5;MQ=55.92;MQ0=0;MQRankSum=0.892;QD=12.7;ReadPosRankSum=-2.082;SOR=0.733;VQSLOD=-0.2447;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:35,28:63:99:879,0,1323 -chr6 58777828 rs11211786 G A 652.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.463;ClippingRankSum=-0.018;DB;DP=77;FS=10.707;MLEAC=1;MLEAF=0.5;MQ=55.75;MQ0=0;MQRankSum=2.081;NEGATIVE_TRAIN_SITE;QD=8.48;ReadPosRankSum=-0.651;SOR=1.322;VQSLOD=-1.674;culprit=QD GT:AD:DP:GQ:PL 0/1:46,26:72:99:681,0,1420 -chr6 58777836 rs9632517 A C 2870.77 PASS AC=2;AF=1.0;AN=2;DB;DP=76;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=55.16;MQ0=0;QD=28.37;SOR=0.811;VQSLOD=2.74;culprit=FS GT:AD:DP:GQ:PL 1/1:0,70:70:99:2899,214,0 -chr6 58777939 rs9632518 G A 2463.77 PASS AC=2;AF=1.0;AN=2;DB;DP=65;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=44.89;MQ0=0;QD=25.14;SOR=1.143;VQSLOD=4.33;culprit=FS GT:AD:DP:GQ:PL 1/1:0,62:62:99:2492,187,0 -chr6 58777952 rs4546514 A G 853.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.23;ClippingRankSum=-1.282;DB;DP=63;FS=2.122;MLEAC=1;MLEAF=0.5;MQ=43.01;MQ0=0;MQRankSum=1.134;QD=13.55;ReadPosRankSum=2.245;SOR=0.46;VQSLOD=1.24;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:28,32:60:99:882,0,851 -chr6 58778001 . G A 533.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-2.458;ClippingRankSum=-0.8;DP=68;FS=0.981;MLEAC=1;MLEAF=0.5;MQ=45.56;MQ0=0;MQRankSum=-0.598;QD=7.85;ReadPosRankSum=0.699;SOR=0.563;VQSLOD=-0.063;culprit=QD GT:AD:DP:GQ:PL 0/1:41,22:63:99:562,0,1296 -chr6 58778019 rs9638027 T G 165.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=2.004;ClippingRankSum=-1.301;DB;DP=72;FS=1.422;MLEAC=1;MLEAF=0.5;MQ=45.92;MQ0=0;MQRankSum=1.339;NEGATIVE_TRAIN_SITE;QD=2.3;ReadPosRankSum=0.522;SOR=1.106;VQSLOD=-1.041;culprit=QD GT:AD:DP:GQ:PL 0/1:56,9:65:99:194,0,2191 -chr6 58778025 rs9638028 A G 2317.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.876;ClippingRankSum=-0.113;DB;DP=72;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=45.27;MQ0=0;MQRankSum=-0.523;QD=32.19;ReadPosRankSum=0.277;SOR=0.604;VQSLOD=0.716;culprit=FS GT:AD:DP:GQ:PL 0/1:7,60:67:99:2346,0,110 -chr6 58778036 rs9404685 A C 534.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.105;ClippingRankSum=-1.103;DB;DP=69;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=44.49;MQ0=0;MQRankSum=-0.499;QD=7.75;ReadPosRankSum=1.173;SOR=0.668;VQSLOD=2.83;culprit=QD GT:AD:DP:GQ:PL 0/1:38,25:63:99:563,0,1164 -chr6 58778039 rs9638014 G C 2754.77 PASS AC=2;AF=1.0;AN=2;DB;DP=69;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=44.01;MQ0=0;QD=30.33;SOR=0.79;VQSLOD=5.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,63:63:99:2783,190,0 -chr6 58778081 rs4389792 T G 2804.77 PASS AC=2;AF=1.0;AN=2;DB;DP=66;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.55;MQ0=0;QD=36.83;SOR=0.865;VQSLOD=3.57;culprit=QD GT:AD:DP:GQ:PL 1/1:0,61:61:99:2833,190,0 -chr6 58778082 rs4346876 T C 2759.77 PASS AC=2;AF=1.0;AN=2;DB;DP=66;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.55;MQ0=0;QD=35.85;SOR=0.865;VQSLOD=5.04;culprit=QD GT:AD:DP:GQ:PL 1/1:0,61:61:99:2788,187,0 -chr6 58778100 rs9391506 A T 94.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.077;ClippingRankSum=-0.536;DB;DP=63;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=49.08;MQ0=0;MQRankSum=-0.098;QD=1.5;ReadPosRankSum=-0.93;SOR=0.801;VQSLOD=0.858;culprit=QD GT:AD:DP:GQ:PL 0/1:48,9:57:99:123,0,1551 -chr6 58778108 rs4308591 G C 2796.77 PASS AC=2;AF=1.0;AN=2;DB;DP=68;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=51.2;MQ0=0;QD=21.44;SOR=1.092;VQSLOD=3.79;culprit=FS GT:AD:DP:GQ:PL 1/1:0,63:63:99:2825,196,0 -chr6 58778145 rs9500568 T C 228.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=1.501;ClippingRankSum=0.435;DB;DP=69;FS=1.229;MLEAC=1;MLEAF=0.5;MQ=55.74;MQ0=0;MQRankSum=0.074;QD=3.32;ReadPosRankSum=0.631;SOR=0.425;VQSLOD=-0.7171;culprit=QD GT:AD:DP:GQ:PL 0/1:52,13:65:99:257,0,1648 -chr6 58778148 rs12213271 T C 43.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.529;ClippingRankSum=0.21;DB;DP=69;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.74;MQ0=0;MQRankSum=-2.466;NEGATIVE_TRAIN_SITE;QD=0.63;ReadPosRankSum=-1.168;SOR=0.796;VQSLOD=-1.747;culprit=QD GT:AD:DP:GQ:PL 0/1:57,8:65:72:72,0,1899 -chr6 58778190 rs9767581 T G 325.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=2.002;ClippingRankSum=-0.571;DB;DP=71;FS=1.103;MLEAC=1;MLEAF=0.5;MQ=57.28;MQ0=0;MQRankSum=0.86;QD=4.59;ReadPosRankSum=0.34;SOR=0.886;VQSLOD=-0.4734;culprit=QD GT:AD:DP:GQ:PL 0/1:52,16:68:99:354,0,1641 -chr6 58778207 rs6588729 G A 2273.77 VQSRTrancheSNP99.00to99.90 AC=2;AF=1.0;AN=2;BaseQRankSum=1.676;ClippingRankSum=-1.397;DB;DP=65;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.24;MQ0=0;MQRankSum=0.95;NEGATIVE_TRAIN_SITE;QD=34.98;ReadPosRankSum=-1.341;SOR=0.236;VQSLOD=-1.078;culprit=QD GT:AD:DP:GQ:PL 1/1:1,61:62:99:2302,182,0 -chr6 58778244 rs6588730 A T 2044.77 PASS AC=2;AF=1.0;AN=2;DB;DP=65;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=56.41;MQ0=0;QD=31.46;SOR=0.76;VQSLOD=4.48;culprit=FS GT:AD:DP:GQ:PL 1/1:0,60:60:99:2073,180,0 -chr6 58778404 rs6588731 C A 2347.77 PASS AC=2;AF=1.0;AN=2;DB;DP=57;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=52.8;MQ0=0;QD=32.04;SOR=0.808;VQSLOD=5.86;culprit=FS GT:AD:DP:GQ:PL 1/1:0,53:53:99:2376,160,0 -chr6 58778405 rs6588732 C T 2392.77 PASS AC=2;AF=1.0;AN=2;DB;DP=56;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=52.66;MQ0=0;QD=27.48;SOR=0.77;VQSLOD=4.38;culprit=FS GT:AD:DP:GQ:PL 1/1:0,52:52:99:2421,163,0 -chr6 58778412 rs6588733 T C 2705.77 PASS AC=2;AF=1.0;AN=2;DB;DP=62;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.42;MQ0=0;QD=34.01;SOR=0.762;VQSLOD=5.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,58:58:99:2734,184,0 -chr6 58778452 rs4928629 A C 970.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.809;ClippingRankSum=-0.744;DB;DP=64;FS=5.099;MLEAC=1;MLEAF=0.5;MQ=55.54;MQ0=0;MQRankSum=2.13;POSITIVE_TRAIN_SITE;QD=15.17;ReadPosRankSum=1.163;SOR=1.249;VQSLOD=1.86;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:29,32:61:99:999,0,986 -chr6 58778456 . G T 154.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.779;ClippingRankSum=-0.534;DP=68;FS=2.839;MLEAC=1;MLEAF=0.5;MQ=55.81;MQ0=0;MQRankSum=1.216;NEGATIVE_TRAIN_SITE;QD=2.28;ReadPosRankSum=0.079;SOR=0.654;VQSLOD=-0.8069;culprit=QD GT:AD:DP:GQ:PL 0/1:54,11:65:99:183,0,2074 -chr6 58778482 rs6588734 G A 2628.77 PASS AC=2;AF=1.0;AN=2;DB;DP=64;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=55.61;MQ0=0;QD=31.77;SOR=0.906;VQSLOD=3.8;culprit=FS GT:AD:DP:GQ:PL 1/1:0,60:60:99:2657,190,0 -chr6 58778519 rs4928633 A G 847.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.545;ClippingRankSum=-1.803;DB;DP=75;FS=6.752;MLEAC=1;MLEAF=0.5;MQ=54.72;MQ0=0;MQRankSum=-1.213;QD=11.3;ReadPosRankSum=0.443;SOR=1.183;VQSLOD=-0.4825;culprit=FS GT:AD:DP:GQ:PL 0/1:44,24:68:99:876,0,1700 -chr6 58778530 rs9647643 T C 919.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=3.069;ClippingRankSum=-0.13;DB;DP=71;FS=8.855;MLEAC=1;MLEAF=0.5;MQ=54.76;MQ0=0;MQRankSum=-0.936;QD=12.95;ReadPosRankSum=-0.567;SOR=1.363;VQSLOD=-0.0751;culprit=FS GT:AD:DP:GQ:PL 0/1:38,26:64:99:948,0,1688 -chr6 58778531 rs9647644 A C 922.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.99;ClippingRankSum=0.934;DB;DP=70;FS=8.966;MLEAC=1;MLEAF=0.5;MQ=54.68;MQ0=0;MQRankSum=-1.454;QD=13.18;ReadPosRankSum=-0.204;SOR=1.572;VQSLOD=-0.337;culprit=FS GT:AD:DP:GQ:PL 0/1:38,25:63:99:951,0,1651 -chr6 58778577 rs6588735 T A 348.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.086;ClippingRankSum=0.432;DB;DP=70;FS=8.999;MLEAC=1;MLEAF=0.5;MQ=54.75;MQ0=0;MQRankSum=-0.934;NEGATIVE_TRAIN_SITE;QD=4.98;ReadPosRankSum=0.225;SOR=0.956;VQSLOD=-2.51;culprit=QD GT:AD:DP:GQ:PL 0/1:49,13:62:99:377,0,2028 -chr6 58778584 rs6588736 T G 310.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-2.597;ClippingRankSum=0.859;DB;DP=67;FS=2.94;MLEAC=1;MLEAF=0.5;MQ=54.51;MQ0=0;MQRankSum=0.896;QD=4.64;ReadPosRankSum=0.545;SOR=0.275;VQSLOD=-0.1432;culprit=QD GT:AD:DP:GQ:PL 0/1:48,12:60:99:339,0,2037 -chr6 58778664 rs112323615 T G 597.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=0.932;ClippingRankSum=-0.755;DB;DP=68;FS=5.051;MLEAC=1;MLEAF=0.5;MQ=57.08;MQ0=0;MQRankSum=0.959;QD=8.79;ReadPosRankSum=-0.864;SOR=0.98;VQSLOD=-0.2673;culprit=QD GT:AD:DP:GQ:PL 0/1:44,22:66:99:626,0,1333 -chr6 58778716 rs7453620 A C 1189.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=0.027;ClippingRankSum=-0.97;DB;DP=79;FS=6.175;MLEAC=1;MLEAF=0.5;MQ=57.55;MQ0=0;MQRankSum=-0.769;QD=15.06;ReadPosRankSum=-1.098;SOR=0.261;VQSLOD=0.195;culprit=FS GT:AD:DP:GQ:PL 0/1:36,39:75:99:1218,0,1070 -chr6 58778747 rs12214947 T C 88.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-1.524;ClippingRankSum=-1.054;DB;DP=88;FS=4.622;MLEAC=1;MLEAF=0.5;MQ=58.67;MQ0=0;MQRankSum=0.705;NEGATIVE_TRAIN_SITE;QD=1.01;ReadPosRankSum=1.189;SOR=0.575;VQSLOD=-2.375;culprit=QD GT:AD:DP:GQ:PL 0/1:72,11:83:99:117,0,2437 -chr6 58778788 rs6651013 T C 3397.77 PASS AC=2;AF=1.0;AN=2;DB;DP=99;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.86;MQ0=0;QD=34.32;SOR=0.976;VQSLOD=4.25;culprit=FS GT:AD:DP:GQ:PL 1/1:0,94:94:99:3426,282,0 -chr6 58778844 rs7452594 C G 898.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=0.445;ClippingRankSum=-0.341;DB;DP=82;FS=12.217;MLEAC=1;MLEAF=0.5;MQ=58.57;MQ0=0;MQRankSum=0.289;QD=10.96;ReadPosRankSum=1.634;SOR=1.334;VQSLOD=-0.6564;culprit=FS GT:AD:DP:GQ:PL 0/1:49,29:78:99:927,0,1649 -chr6 58778922 rs6651011 C A 2529.77 VQSRTrancheSNP99.00to99.90 AC=2;AF=1.0;AN=2;BaseQRankSum=1.683;ClippingRankSum=1.147;DB;DP=74;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.77;MQ0=0;MQRankSum=1.586;NEGATIVE_TRAIN_SITE;QD=34.19;ReadPosRankSum=-0.952;SOR=0.246;VQSLOD=-1.389;culprit=FS GT:AD:DP:GQ:PL 1/1:1,70:71:99:2558,204,0 -chr6 58778989 rs6651015 T C 2986.77 PASS AC=2;AF=1.0;AN=2;DB;DP=74;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.71;MQ0=0;QD=37.21;SOR=0.722;VQSLOD=4.76;culprit=QD GT:AD:DP:GQ:PL 1/1:0,69:69:99:3015,208,0 -chr6 58779007 rs6651016 C T 3187.77 PASS AC=2;AF=1.0;AN=2;DB;DP=78;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=58.13;MQ0=0;QD=33.52;SOR=0.836;VQSLOD=5.6;culprit=FS GT:AD:DP:GQ:PL 1/1:0,73:73:99:3216,223,0 -chr6 58779056 rs6937914 T C 824.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.434;ClippingRankSum=0.011;DB;DP=75;FS=0.903;MLEAC=1;MLEAF=0.5;MQ=59.19;MQ0=0;MQRankSum=-1.194;QD=11.0;ReadPosRankSum=0.535;SOR=0.535;VQSLOD=0.407;culprit=FS GT:AD:DP:GQ:PL 0/1:41,31:72:99:853,0,1368 -chr6 58779089 rs4286808 C A 635.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=2.994;ClippingRankSum=-1.111;DB;DP=63;FS=14.811;MLEAC=1;MLEAF=0.5;MQ=58.97;MQ0=0;MQRankSum=-0.125;NEGATIVE_TRAIN_SITE;QD=10.09;ReadPosRankSum=0.169;SOR=1.477;VQSLOD=-1.459;culprit=FS GT:AD:DP:GQ:PL 0/1:40,22:62:99:664,0,1572 -chr6 58779097 rs9500231 A G 1804.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-0.594;ClippingRankSum=1.075;DB;DP=68;FS=2.521;MLEAC=1;MLEAF=0.5;MQ=58.76;MQ0=0;MQRankSum=-0.173;QD=26.54;ReadPosRankSum=0.414;SOR=0.501;VQSLOD=-0.2854;culprit=DP GT:AD:DP:GQ:PL 0/1:15,52:67:99:1833,0,403 -chr6 58779308 rs6651018 T C 16.86 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-1.004;ClippingRankSum=-0.972;DB;DP=51;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=45.75;MQ0=0;MQRankSum=-0.526;QD=0.33;ReadPosRankSum=0.43;SOR=0.783 GT:AD:DP:GQ:PL 0/1:42,6:48:45:45,0,1235 -chr6 58779328 rs6651019 A G 1227.77 VQSRTrancheSNP99.00to99.90 AC=2;AF=1.0;AN=2;BaseQRankSum=0.974;ClippingRankSum=-1.31;DB;DP=39;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=43.52;MQ0=0;MQRankSum=0.772;QD=31.48;ReadPosRankSum=1.511;SOR=1.675;VQSLOD=0.201;culprit=FS GT:AD:DP:GQ:PL 1/1:2,35:37:38:1256,38,0 -chr6 58779346 rs4376372 T G 350.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.662;ClippingRankSum=-0.5;DB;DP=32;FS=2.071;MLEAC=1;MLEAF=0.5;MQ=39.86;MQ0=0;MQRankSum=0.46;QD=10.96;ReadPosRankSum=-0.5;SOR=1.292;VQSLOD=1.45;culprit=QD GT:AD:DP:GQ:PL 0/1:18,13:31:99:379,0,605 -chr6 58779375 rs4250419 A G 273.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.795;ClippingRankSum=-0.971;DB;DP=18;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=30.82;MQ0=0;MQRankSum=-0.442;QD=15.21;ReadPosRankSum=-1.589;SOR=1.781;VQSLOD=3.91;culprit=FS GT:AD:DP:GQ:PL 0/1:9,9:18:99:302,0,370 -chr6 58779376 rs6651020 C T 736.77 PASS AC=2;AF=1.0;AN=2;DB;DP=17;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=30.93;MQ0=0;QD=27.25;SOR=4.294;VQSLOD=5.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,17:17:54:765,54,0 -chr6 58779409 rs4400241 T C 160.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.793;ClippingRankSum=1.461;DB;DP=12;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=32.29;MQ0=0;MQRankSum=0.529;QD=13.4;ReadPosRankSum=1.788;SOR=1.371;VQSLOD=4.57;culprit=FS GT:AD:DP:GQ:PL 0/1:7,5:12:99:189,0,263 -chr6 58779468 rs6651021 A G 83.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=30.9;MQ0=0;MQRankSum=-0.727;QD=20.94;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=4.64;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:28:112,0,28 -chr6 58779499 rs6651022 T C 49.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=29.0;MQ0=0;MQRankSum=-1.026;QD=12.44;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=4.09;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:54:78,0,54 -chr6 61892431 rs4467815 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 61909056 rs189688252 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 61924395 rs74442497 A C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 61924424 rs149028611 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 61939361 rs76899121 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 61967504 rs704487 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 61967842 rs79961499 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 61984979 . G T 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:34:40,0,34 -chr6 62017935 rs1997843 T C 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=9.5;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 62024599 rs1414786 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62027240 rs1074429 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62034435 rs115639864 C T 36.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.988;ClippingRankSum=0.406;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.04;MQ0=0;MQRankSum=0.406;QD=6.13;ReadPosRankSum=-0.406;SOR=0.693;VQSLOD=4.21;culprit=QD GT:AD:DP:GQ:PL 0/1:3,3:6:65:65,0,104 -chr6 62084214 rs3908837 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62114785 rs7742522 T G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62183331 rs2092608 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62183845 rs35300708 C CT 19.75 LowQual AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=6.58;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:56,6,0 -chr6 62198757 rs6916640 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62208255 rs116736672 G A 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.86;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 62217827 rs415716 G T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62220171 rs387256 A T 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 62233173 rs214151 G C 71.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=41.3;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.02;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 -chr6 62236450 rs116060945 A T 18.8 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=9.4;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:46,6,0 -chr6 62252108 rs4598053 C A 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.68;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 62252188 rs67145854 GA G 75.25 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.08;SOR=1.179;VQSLOD=8.13;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:112,9,0 -chr6 62269382 rs59519746 T C 18.59 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=18.59;SOR=1.609;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 62269405 rs56095991 G T 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=7.79;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 62290945 rs140805963 G A 44.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=5.79;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 0/1:1,2:3:31:73,0,31 -chr6 62294589 rs115452241 T C 55.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.43;SOR=1.179;VQSLOD=6.13;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,3:3:9:83,9,0 -chr6 62316285 rs213776 A C 47.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.0;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=11.94;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=5.88;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 0/1:2,2:4:67:76,0,67 -chr6 62329027 rs201975337 A AT 15.82 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=7.91;SOR=0.693;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:52,6,0 -chr6 62390916 rs1204114 T C 2091.77 PASS AC=2;AF=1.0;AN=2;DB;DP=56;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.71;SOR=0.765;VQSLOD=6.9;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,56:56:99:2120,168,0 -chr6 62413546 rs1204139 A C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62495041 rs78507898 T A 20.78 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.39;SOR=0.693;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:48,6,0 -chr6 62510310 rs1743448 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62515335 . C A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62532253 rs571607 G C 60.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=0.693;VQSLOD=9.11;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:88,6,0 -chr6 62582748 . G T 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223;GENE=KHDRBS2 GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 -chr6 62604848 . T TTC 69.25 PASS AC=2;AF=1.0;AN=2;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=55.21;MQ0=0;QD=13.85;SOR=2.303;VQSLOD=5.37;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:9:106,9,0 -chr6 62650334 rs1114027 T A 48.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=8.08;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 62674103 rs1192455 C T 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=9.36;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 62674110 rs1192454 G A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.92;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 62686434 rs1192430 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62690574 rs1393669 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62706684 rs2102790 C T 48.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=7.03;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 62708691 rs9453889 C A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=KHDRBS2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62757987 rs9346001 C T 744.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.533;ClippingRankSum=0.028;DB;DP=52;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.661;POSITIVE_TRAIN_SITE;QD=14.32;ReadPosRankSum=1.294;SOR=0.546;VQSLOD=5.4;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 0/1:28,24:52:99:773,0,900 -chr6 62886921 rs10455666 C T 184.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.067;ClippingRankSum=-0.572;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.067;POSITIVE_TRAIN_SITE;QD=23.1;ReadPosRankSum=-0.572;SOR=1.863;VQSLOD=6.13;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 0/1:2,6:8:59:213,0,59 -chr6 62887031 rs9346218 C T 1086.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.596;ClippingRankSum=1.848;DB;DP=62;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.846;POSITIVE_TRAIN_SITE;QD=17.53;ReadPosRankSum=-0.056;SOR=0.846;VQSLOD=5.07;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 0/1:29,33:62:99:1115,0,921 -chr6 62887099 rs6921170 C T 1783.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.393;ClippingRankSum=0.055;DB;DP=121;FS=0.706;MLEAC=1;MLEAF=0.5;MQ=59.85;MQ0=0;MQRankSum=0.039;POSITIVE_TRAIN_SITE;QD=14.74;ReadPosRankSum=-0.465;SOR=0.841;VQSLOD=2.95;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 0/1:60,60:120:99:1812,0,2047 -chr6 62995920 rs16883133 T G 157.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.0;ClippingRankSum=-0.572;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=19.72;ReadPosRankSum=1.067;SOR=0.693;VQSLOD=6.06;culprit=FS;GENE=KHDRBS2 GT:AD:DP:GQ:PL 0/1:2,6:8:55:186,0,55 -chr6 63018890 rs9354897 A G 47.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.76;SOR=1.179;VQSLOD=7.6;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:75,9,0 -chr6 63022153 rs523967 G A 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=9.05;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 63022286 rs62414811 G A 58.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=8.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 63046505 rs508263 T C 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.8;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 63104500 rs2814661 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63116886 rs2452472 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63123748 rs2814696 C A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63139149 rs2452463 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63167529 rs2881136 G A 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 63171060 rs17381471 C T 645.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.586;ClippingRankSum=-0.249;DB;DP=71;FS=9.277;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.188;POSITIVE_TRAIN_SITE;QD=9.1;ReadPosRankSum=-0.067;SOR=2.159;VQSLOD=0.69;culprit=QD;GENE=DHFRP5 GT:AD:DP:GQ:PL 0/1:47,24:71:99:674,0,1531 -chr6 63171544 rs648165 A T 113.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.72;ClippingRankSum=-0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.38;POSITIVE_TRAIN_SITE;QD=18.96;ReadPosRankSum=1.38;SOR=1.329;VQSLOD=6.18;culprit=FS;GENE=DHFRP5 GT:AD:DP:GQ:PL 0/1:2,4:6:62:142,0,62 -chr6 63251196 rs2345983 C T 109.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.937;ClippingRankSum=-0.55;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.62;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=15.68;ReadPosRankSum=-0.55;SOR=0.941;VQSLOD=6.88;culprit=FS GT:AD:DP:GQ:PL 0/1:3,4:7:90:138,0,90 -chr6 63257354 rs9446610 C T 1142.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.489;ClippingRankSum=-0.017;DB;DP=75;FS=1.132;MLEAC=1;MLEAF=0.5;MQ=58.43;MQ0=0;MQRankSum=-0.447;POSITIVE_TRAIN_SITE;QD=15.24;ReadPosRankSum=0.337;SOR=0.935;VQSLOD=3.19;culprit=FS GT:AD:DP:GQ:PL 0/1:38,35:73:99:1171,0,1224 -chr6 63257971 rs6913632 T C 1383.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.999;ClippingRankSum=0.127;DB;DP=63;FS=2.484;MLEAC=1;MLEAF=0.5;MQ=59.21;MQ0=0;MQRankSum=1.565;POSITIVE_TRAIN_SITE;QD=21.96;ReadPosRankSum=-0.367;SOR=0.382;VQSLOD=1.73;culprit=QD GT:AD:DP:GQ:PL 0/1:19,44:63:99:1412,0,451 -chr6 63258233 rs11447029 C CA 15.85 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.718;ClippingRankSum=-1.371;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=58.55;MQ0=0;MQRankSum=-0.065;QD=0.99;ReadPosRankSum=0.588;SOR=0.16 GT:AD:DP:GQ:PL 0/1:11,4:15:53:53,0,220 -chr6 63290332 rs9351926 C A 41.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=13.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=5.99;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:36:70,0,36 -chr6 63309881 rs73762312 G T 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.61;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 63356605 rs4710365 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63357734 rs66885289 CTT C 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=7.46;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 63370591 rs7776261 C A 49.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=8.45;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 63370651 rs7761764 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63394799 rs4131720 C A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63426649 rs2752973 C T 43.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.59;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=2.74;culprit=DP GT:AD:DP:GQ:PL 0/1:1,2:3:32:72,0,32 -chr6 63480621 rs6937512 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63508240 rs4710370 A C 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.3;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 63508253 rs4710371 T A 14.68 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=14.68;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:41,3,0 -chr6 63520794 rs7746171 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63522176 rs9352169 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63567509 rs11961562 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63576005 rs55851245 C G 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 63584587 rs12207161 G A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.52;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 63584592 rs12208504 G A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.23;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 63596076 rs7747071 G A 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=8.75;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 63596112 rs4307155 C T 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=7.9;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 63607258 rs10943283 C A 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=9.09;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 63727757 rs9343533 C A 287.78 PASS AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.82;SOR=2.833;VQSLOD=6.93;culprit=FS GT:AD:DP:GQ:PL 1/1:0,8:8:24:316,24,0 -chr6 63730222 rs9352418 G T 61.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 -chr6 63730266 rs9343536 T C 47.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=0.693;VQSLOD=8.81;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 63733880 rs10943404 G T 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=2.303;VQSLOD=8.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 63749658 rs6936280 A G 59.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.69;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 63749860 rs6941288 T C 49.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=24.87;SOR=0.693;VQSLOD=4.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 63753907 rs12208886 A G 62.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.6;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 63757242 . G T 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63775888 rs789964 A T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63785384 rs789954 G A 48.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=7.8;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 63792401 rs1086295 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63863011 rs57238578 G GGTTGTT 44.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=2.303;VQSLOD=8.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 63874309 rs9343765 G A 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=28.87;SOR=2.303;VQSLOD=7.35;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 63874499 rs7747081 C T 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.58;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 63885713 rs3059784 T TTG 26.71 LowQual AC=2;AF=1.0;AN=2;DB;DP=1;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.71;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:6:63,6,0 -chr6 63885782 rs1020805 T G 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.09;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 63902995 rs1847501 G T 1552.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=6.223;ClippingRankSum=0.5;DB;DP=79;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.817;POSITIVE_TRAIN_SITE;QD=19.66;ReadPosRankSum=-0.005;SOR=0.743;VQSLOD=4.99;culprit=FS GT:AD:DP:GQ:PL 0/1:34,45:79:99:1581,0,943 -chr6 63903354 rs16893840 G T 550.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.19;ClippingRankSum=0.804;DB;DP=38;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.89;MQ0=0;MQRankSum=-0.219;POSITIVE_TRAIN_SITE;QD=14.49;ReadPosRankSum=0.57;SOR=0.754;VQSLOD=5.91;culprit=FS GT:AD:DP:GQ:PL 0/1:20,18:38:99:579,0,671 -chr6 63903377 rs6914331 G A 1128.77 PASS AC=2;AF=1.0;AN=2;DB;DP=28;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=54.85;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.22;SOR=1.609;VQSLOD=5.16;culprit=FS GT:AD:DP:GQ:PL 1/1:0,28:28:84:1157,84,0 -chr6 63903384 rs2047899 G T 382.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.034;ClippingRankSum=-0.528;DB;DP=28;FS=1.69;MLEAC=1;MLEAF=0.5;MQ=53.95;MQ0=0;MQRankSum=-1.08;POSITIVE_TRAIN_SITE;QD=13.67;ReadPosRankSum=0.345;SOR=0.269;VQSLOD=2.91;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:14,14:28:99:411,0,430 -chr6 63903574 rs142293404 GAAGGAGC G 121.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.754;ClippingRankSum=1.754;DB;DP=8;FS=3.68;MLEAC=1;MLEAF=0.5;MQ=47.12;MQ0=0;MQRankSum=-1.754;QD=15.22;ReadPosRankSum=0.0;SOR=2.494;VQSLOD=0.824;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:3,4:7:99:159,0,331 -chr6 63903606 rs116456502 G A 133.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.72;ClippingRankSum=0.0;DB;DP=6;FS=4.771;MLEAC=1;MLEAF=0.5;MQ=41.96;MQ0=0;MQRankSum=-1.38;POSITIVE_TRAIN_SITE;QD=22.29;ReadPosRankSum=1.231;SOR=3.258;VQSLOD=1.17;culprit=DP GT:AD:DP:GQ:PL 0/1:2,4:6:99:162,0,243 -chr6 63921361 rs4710420 A G 237.78 PASS AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.72;SOR=4.407;VQSLOD=7.22;culprit=FS;GENE=FKBP1C GT:AD:DP:GQ:PL 1/1:0,8:8:24:266,24,0 -chr6 63921442 rs76273486 G A 318.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.127;ClippingRankSum=-0.433;DB;DP=17;FS=3.274;MLEAC=1;MLEAF=0.5;MQ=51.85;MQ0=0;MQRankSum=2.261;POSITIVE_TRAIN_SITE;QD=18.75;ReadPosRankSum=1.299;SOR=1.981;VQSLOD=1.5;culprit=MQRankSum;GENE=FKBP1C GT:AD:DP:GQ:PL 0/1:8,9:17:99:347,0,251 -chr6 63921456 rs79100944 G A 493.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.628;ClippingRankSum=-0.102;DB;DP=22;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.18;MQ0=0;MQRankSum=1.74;QD=22.44;ReadPosRankSum=1.604;SOR=1.402;VQSLOD=0.39;culprit=FS;GENE=FKBP1C GT:AD:DP:GQ:PL 0/1:8,14:22:99:522,0,233 -chr6 63921924 rs9359357 A G 278.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.409;ClippingRankSum=-1.184;DB;DP=19;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=54.85;MQ0=0;MQRankSum=-1.347;QD=14.67;ReadPosRankSum=1.266;SOR=1.609;VQSLOD=3.62;culprit=FS;GENE=FKBP1C GT:AD:DP:GQ:PL 0/1:10,9:19:99:307,0,291 -chr6 63933615 rs9352684 A T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63937797 rs12526013 T C 105.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.116;ClippingRankSum=-0.735;DB;DP=23;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=41.41;MQ0=0;MQRankSum=-0.385;POSITIVE_TRAIN_SITE;QD=4.6;ReadPosRankSum=0.175;SOR=0.141;VQSLOD=3.69;culprit=QD;GENE=SPTLC1P3 GT:AD:DP:GQ:PL 0/1:17,6:23:99:134,0,553 -chr6 63937863 rs3925806 T C 119.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.38;ClippingRankSum=0.72;DB;DP=6;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.51;MQ0=0;MQRankSum=0.72;POSITIVE_TRAIN_SITE;QD=19.96;ReadPosRankSum=0.72;SOR=0.368;VQSLOD=6.05;culprit=FS;GENE=SPTLC1P3 GT:AD:DP:GQ:PL 0/1:2,4:6:60:148,0,60 -chr6 63937916 rs3925805 A C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.0;MQ0=0;QD=10.88;SOR=0.693;GENE=SPTLC1P3 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63939795 rs1809272 T C 2647.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=-6.907;ClippingRankSum=0.336;DB;DP=202;FS=8.305;MLEAC=1;MLEAF=0.5;MQ=53.46;MQ0=0;MQRankSum=-3.258;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=13.11;ReadPosRankSum=-0.632;SOR=0.35;VQSLOD=-0.4749;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:107,93:200:99:2676,0,3595 -chr6 63939829 rs1809271 A T 8543.77 PASS AC=2;AF=1.0;AN=2;DB;DP=238;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=52.9;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.91;SOR=0.925;VQSLOD=3.77;culprit=QD GT:AD:DP:GQ:PL 1/1:0,237:237:99:8572,713,0 -chr6 63940061 rs4035417 A G 1171.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=2.262;ClippingRankSum=-0.144;DB;DP=64;FS=5.367;MLEAC=1;MLEAF=0.5;MQ=51.76;MQ0=0;MQRankSum=-3.916;NEGATIVE_TRAIN_SITE;QD=18.31;ReadPosRankSum=1.606;SOR=0.207;VQSLOD=-1.9;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:26,38:64:99:1200,0,790 -chr6 63940313 rs6905048 A C 40.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;QD=20.37;SOR=2.303;VQSLOD=6.78;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 63969766 rs9352729 A G 60.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=30.37;SOR=2.303;VQSLOD=7.74;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:88,6,0 -chr6 63990648 rs35296992 A G 956.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.261;ClippingRankSum=-0.057;DB;DP=88;FS=2.946;MLEAC=1;MLEAF=0.5;MQ=59.79;MQ0=0;MQRankSum=-0.678;POSITIVE_TRAIN_SITE;QD=10.87;ReadPosRankSum=-0.582;SOR=0.521;VQSLOD=1.69;culprit=QD;GENE=LGSN GT:AD:DP:GQ:PL 0/1:54,33:87:99:985,0,1782 -chr6 64126837 rs149978231 T TAC 29.71 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;QD=14.85;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:66,6,0 -chr6 64147016 rs144385019 AAGAAAGGGAGAAGGAAAAGAAAGAAAGG A 85.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=39.12;MQ0=0;MQRankSum=-0.727;QD=21.43;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=5.01;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:99:123,0,203 -chr6 64150689 rs10755410 G A 62.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.404;ClippingRankSum=-0.74;DB;DP=13;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.185;POSITIVE_TRAIN_SITE;QD=4.83;ReadPosRankSum=1.849;SOR=0.582;VQSLOD=4.9;culprit=QD GT:AD:DP:GQ:PL 0/1:9,3:12:91:91,0,260 -chr6 64151093 rs9361767 A G 149.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.572;ClippingRankSum=1.067;DB;DP=8;FS=3.332;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.572;POSITIVE_TRAIN_SITE;QD=18.72;ReadPosRankSum=-1.589;SOR=0.105;VQSLOD=1.98;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:2,6:8:54:178,0,54 -chr6 64151771 rs9294215 C G 107.78 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.731;ClippingRankSum=0.731;DB;DP=5;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.731;POSITIVE_TRAIN_SITE;QD=21.56;ReadPosRankSum=0.731;SOR=1.981;VQSLOD=6.52;culprit=FS GT:AD:DP:GQ:PL 0/1:1,4:5:25:136,0,25 -chr6 64153691 rs2076874 G A 46.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.37;SOR=2.303;VQSLOD=8.47;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:74,6,0 -chr6 64189643 rs58741217 T TCAAA 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=7.13;culprit=FS;GENE=EEF1B2P5 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 64190067 rs9443931 C A 393.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.203;ClippingRankSum=-0.958;DB;DP=27;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.575;POSITIVE_TRAIN_SITE;QD=14.58;ReadPosRankSum=-1.068;SOR=0.795;VQSLOD=5.07;culprit=FS;GENE=EEF1B2P5 GT:AD:DP:GQ:PL 0/1:11,14:25:99:422,0,388 -chr6 64190278 rs2622276 A T 386.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.855;ClippingRankSum=-0.153;DB;DP=29;FS=1.455;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.065;POSITIVE_TRAIN_SITE;QD=13.34;ReadPosRankSum=-1.637;SOR=1.112;VQSLOD=2.78;culprit=ReadPosRankSum;GENE=EEF1B2P5 GT:AD:DP:GQ:PL 0/1:14,15:29:99:415,0,464 -chr6 64190446 rs4299811 C T 145.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.322;ClippingRankSum=0.684;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.322;POSITIVE_TRAIN_SITE;QD=18.22;ReadPosRankSum=0.956;SOR=0.33;VQSLOD=6.88;culprit=FS;GENE=EEF1B2P5 GT:AD:DP:GQ:PL 0/1:3,5:8:87:174,0,87 -chr6 64190547 rs4557499 G T 91.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=2.833;VQSLOD=8.49;culprit=FS;GENE=EEF1B2P5 GT:AD:DP:GQ:PL 1/1:0,3:3:9:119,9,0 -chr6 64191578 rs10943822 A T 30.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.001;ClippingRankSum=0.248;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.248;POSITIVE_TRAIN_SITE;QD=3.42;ReadPosRankSum=0.248;SOR=0.223;VQSLOD=4.86;culprit=QD;GENE=EEF1B2P5 GT:AD:DP:GQ:PL 0/1:6,3:9:59:59,0,364 -chr6 64191586 rs10943823 T C 73.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.566;ClippingRankSum=-0.382;DB;DP=11;FS=3.09;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.566;POSITIVE_TRAIN_SITE;QD=6.71;ReadPosRankSum=0.715;SOR=0.132;VQSLOD=1.93;culprit=QD;GENE=EEF1B2P5 GT:AD:DP:GQ:PL 0/1:8,3:11:99:102,0,417 -chr6 64191949 rs2800052 C T 95.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=2.833;VQSLOD=7.66;culprit=FS;GENE=EEF1B2P5 GT:AD:DP:GQ:PL 1/1:0,3:3:9:123,9,0 -chr6 64209875 rs1744139 G A 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.83;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 64209877 rs1779772 T G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.4;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 64221239 rs1744145 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64239405 rs1681942 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=PTP4A1 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64258654 rs1744153 C T 990.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-3.025;ClippingRankSum=1.004;DB;DP=65;FS=1.109;MLEAC=1;MLEAF=0.5;MQ=59.65;MQ0=0;MQRankSum=0.846;POSITIVE_TRAIN_SITE;QD=15.24;ReadPosRankSum=1.161;SOR=0.907;VQSLOD=3.16;culprit=FS;GENE=RPL7AP34,PTP4A1 GT:AD:DP:GQ:PL 0/1:32,33:65:99:1019,0,1066 -chr6 64289938 . AT A 167.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.598;ClippingRankSum=0.045;DP=221;FS=3.21;MLEAC=1;MLEAF=0.5;MQ=56.34;MQ0=0;MQRankSum=0.356;QD=0.76;ReadPosRankSum=-0.923;SOR=0.391;VQSLOD=0.248;culprit=DP;GENE=PTP4A1 GT:AD:DP:GQ:PL 0/1:132,35:167:99:205,0,2502 -chr6 64322622 rs34430878 CT C 638.73 PASS AC=2;AF=1.0;AN=2;BaseQRankSum=1.494;ClippingRankSum=-0.777;DB;DP=34;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.64;MQ0=0;MQRankSum=1.255;QD=18.79;ReadPosRankSum=1.614;SOR=5.353;VQSLOD=3.84;culprit=FS GT:AD:DP:GQ:PL 1/1:1,28:29:60:676,60,0 -chr6 64322943 rs4583965 C T 56.84 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=12;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=56.04;MQ0=0;MQRankSum=0.727;QD=4.74;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=3.3;culprit=QD GT:AD:DP:GQ:PL 0/1:1,3:4:18:85,0,18 -chr6 64401952 rs200237690 CATT C 919.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.674;ClippingRankSum=-0.006;DB;DP=77;FS=1.337;MLEAC=1;MLEAF=0.5;MQ=58.29;MQ0=0;MQRankSum=-2.87;POSITIVE_TRAIN_SITE;QD=11.94;ReadPosRankSum=-0.436;SOR=1.105;VQSLOD=1.29;culprit=MQRankSum;GENE=PHF3 GT:AD:DP:GQ:PL 0/1:45,26:71:99:957,0,2148 -chr6 64419024 . CT C 25.74 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-1.086;ClippingRankSum=-2.457;DP=199;FS=4.601;MLEAC=1;MLEAF=0.5;MQ=57.02;MQ0=0;MQRankSum=0.154;QD=0.13;ReadPosRankSum=-0.94;SOR=0.158;GENE=PHF3 GT:AD:DP:GQ:PL 0/1:142,25:167:63:63,0,2866 -chr6 64472270 rs4710257 A C 1520.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.301;ClippingRankSum=-0.541;DB;DP=75;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.155;POSITIVE_TRAIN_SITE;QD=20.28;ReadPosRankSum=-1.387;SOR=0.569;VQSLOD=4.26;culprit=FS;GENE=EYS,PHF3 GT:AD:DP:GQ:PL 0/1:32,43:75:99:1549,0,1031 -chr6 64498933 rs147210136 G A 2218.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.18;ClippingRankSum=0.271;DB;DP=150;FS=9.259;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.467;POSITIVE_TRAIN_SITE;QD=14.79;ReadPosRankSum=1.95;SOR=0.286;VQSLOD=0.949;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:75,74:149:99:2247,0,2088 -chr6 64513363 . C A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64523255 . T C 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64574392 rs10638627 C CTT 140.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.729;ClippingRankSum=0.729;DB;DP=11;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.98;MQ0=0;MQRankSum=0.361;POSITIVE_TRAIN_SITE;QD=12.79;ReadPosRankSum=-0.361;SOR=0.892;VQSLOD=6.6;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:4,5:9:99:178,0,138 -chr6 64574396 rs10645485 T TTC 100.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.219;ClippingRankSum=-0.361;DB;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.361;QD=11.19;ReadPosRankSum=-0.361;SOR=0.527;VQSLOD=4.79;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:5,4:9:99:138,0,178 -chr6 64577850 rs321500 A G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64627882 rs677250 T C 63.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=7.65;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 64686503 rs9362331 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64694354 rs4710457 C T 3197.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.855;ClippingRankSum=1.756;DB;DP=194;FS=1.841;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.786;POSITIVE_TRAIN_SITE;QD=16.48;ReadPosRankSum=2.117;SOR=0.546;VQSLOD=2.3;culprit=DP;GENE=EYS GT:AD:DP:GQ:PL 0/1:92,101:193:99:3226,0,2888 -chr6 64694560 rs1482457 G A 2447.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.451;ClippingRankSum=0.305;DB;DP=164;FS=1.687;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.165;POSITIVE_TRAIN_SITE;QD=14.93;ReadPosRankSum=-0.002;SOR=0.497;VQSLOD=2.46;culprit=DP;GENE=EYS GT:AD:DP:GQ:PL 0/1:89,74:163:99:2476,0,2876 -chr6 64694620 rs1482456 T C 1132.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=5.667;ClippingRankSum=0.22;DB;DP=67;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.663;POSITIVE_TRAIN_SITE;QD=16.91;ReadPosRankSum=2.755;SOR=1.516;VQSLOD=4.16;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:35,32:67:99:1161,0,1169 -chr6 64708907 rs66502009 A C 2569.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=3.193;ClippingRankSum=2.479;DB;DP=165;FS=4.658;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.156;POSITIVE_TRAIN_SITE;QD=15.57;ReadPosRankSum=1.406;SOR=1.162;VQSLOD=1.6;culprit=DP;GENE=EYS GT:AD:DP:GQ:PL 0/1:81,84:165:99:2598,0,2412 -chr6 64752796 rs10944301 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64840987 rs3013170 T C 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=7.79;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 64885636 rs4310034 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64949401 rs35507550 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64966049 rs2057165 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64968295 rs2057160 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64995013 rs6917553 G C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65012918 rs9444712 T C 558.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-4.612;ClippingRankSum=0.176;DB;DP=44;FS=1.724;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.129;POSITIVE_TRAIN_SITE;QD=12.7;ReadPosRankSum=-1.045;SOR=0.412;VQSLOD=2.58;culprit=ReadPosRankSum;GENE=EYS GT:AD:DP:GQ:PL 0/1:22,22:44:99:587,0,721 -chr6 65013122 rs11753319 C G 92.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.368;ClippingRankSum=0.421;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.0;POSITIVE_TRAIN_SITE;QD=11.6;ReadPosRankSum=0.0;SOR=1.609;VQSLOD=6.06;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:4,4:8:99:121,0,142 -chr6 65013202 rs7739082 A C 19.81 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=0.615;ClippingRankSum=-0.168;DB;DP=19;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.01;MQ0=0;MQRankSum=-0.168;QD=1.04;ReadPosRankSum=0.056;SOR=0.495;GENE=EYS GT:AD:DP:GQ:PL 0/1:16,3:19:48:48,0,530 -chr6 65021076 rs1922968 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65031098 rs1922975 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65037680 rs614395 G C 38.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.956;ClippingRankSum=0.322;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.517;POSITIVE_TRAIN_SITE;QD=4.85;ReadPosRankSum=-0.322;SOR=0.818;VQSLOD=4.08;culprit=QD;GENE=EYS GT:AD:DP:GQ:PL 0/1:5,3:8:67:67,0,135 -chr6 65051097 . C T 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65073876 rs671938 G T 51.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=2.303;VQSLOD=8.53;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 65076921 . A G 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65084617 rs4518475 C T 44.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.92;ReadPosRankSum=-0.736;SOR=0.223;VQSLOD=5.99;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:1,2:3:32:73,0,32 -chr6 65168481 rs35441646 C CT 30.71 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.35;SOR=0.693;VQSLOD=8.24;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0 -chr6 65204065 rs13211837 C G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65210797 rs34848022 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65218097 rs9362916 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65229459 rs13202092 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65236845 rs4710276 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65245271 . G C 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65274426 rs140935331 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65302877 rs75420781 A T 134.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-0.198;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.58;MQ0=0;MQRankSum=0.198;POSITIVE_TRAIN_SITE;QD=19.25;ReadPosRankSum=-1.495;SOR=1.609;VQSLOD=5.71;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:2,5:7:61:163,0,61 -chr6 65302898 rs16895524 A G 263.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.313;ClippingRankSum=1.381;DB;DP=13;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=57.97;MQ0=0;MQRankSum=0.533;POSITIVE_TRAIN_SITE;QD=20.29;ReadPosRankSum=0.817;SOR=1.179;VQSLOD=6.63;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:5,8:13:99:292,0,150 -chr6 65302915 rs11331907 GA G 124.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.088;ClippingRankSum=0.971;DB;DP=18;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=55.86;MQ0=0;MQRankSum=-1.678;POSITIVE_TRAIN_SITE;QD=6.93;ReadPosRankSum=2.208;SOR=0.693;VQSLOD=3.97;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:9,9:18:99:162,0,204 -chr6 65302987 rs139235690 ATATCT A 997.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.5;AN=2;BaseQRankSum=2.195;ClippingRankSum=0.287;DB;DP=46;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=47.75;MQ0=0;MQRankSum=-3.55;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=21.69;ReadPosRankSum=3.163;SOR=0.571;VQSLOD=-0.0926;culprit=ReadPosRankSum;GENE=EYS GT:AD:DP:GQ:PL 0/1:19,26:45:99:1035,0,709 -chr6 65303044 rs199667034 T G 104.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.5;AN=2;BaseQRankSum=-5.183;ClippingRankSum=1.517;DB;DP=59;FS=83.06;MLEAC=1;MLEAF=0.5;MQ=52.39;MQ0=0;MQRankSum=0.3;QD=1.78;ReadPosRankSum=-1.257;SOR=5.992;VQSLOD=-11.36;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:40,19:59:99:133,0,1230 -chr6 65303100 rs17404123 T C 1344.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.901;ClippingRankSum=-0.677;DB;DP=82;FS=0.838;MLEAC=1;MLEAF=0.5;MQ=54.84;MQ0=0;MQRankSum=-1.556;POSITIVE_TRAIN_SITE;QD=16.4;ReadPosRankSum=0.481;SOR=0.826;VQSLOD=2.46;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:36,46:82:99:1373,0,1059 -chr6 65303381 rs17290119 T C 46.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=15.59;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=6.6;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:1,2:3:31:75,0,31 -chr6 65305972 rs11759796 G A 55.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.24;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 65318362 rs9445030 C T 61.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.59;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 -chr6 65341959 rs3028242 T TATAAC 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=29.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=8.22;culprit=FS;GENE=EYS,HNRNPDP2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 65365989 rs9445092 T C 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=9.17;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 65369802 rs148392797 C A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65379468 rs1338822 A T 12.05 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223;GENE=EYS GT:AD:DP:GQ:PL 0/1:1,2:3:32:40,0,32 -chr6 65423976 rs9452511 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65430160 rs9354068 C T 53.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=5.09;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 65447951 rs70999169 A AG 84.25 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.08;SOR=1.179;VQSLOD=8.62;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,3:3:9:121,9,0 -chr6 65473673 rs60268597 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65510460 rs34778588 CT C 514.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.895;ClippingRankSum=-0.724;DB;DP=67;FS=1.771;MLEAC=1;MLEAF=0.5;MQ=58.33;MQ0=0;MQRankSum=-0.443;QD=7.68;ReadPosRankSum=1.52;SOR=1.167;VQSLOD=0.651;culprit=ReadPosRankSum;GENE=EYS GT:AD:DP:GQ:PL 0/1:28,30:58:99:552,0,543 -chr6 65523111 rs9345532 A C 67.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.684;ClippingRankSum=0.322;DB;DP=8;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.92;POSITIVE_TRAIN_SITE;QD=8.47;ReadPosRankSum=-0.322;SOR=0.368;VQSLOD=5.25;culprit=QD;GENE=EYS GT:AD:DP:GQ:PL 0/1:5,3:8:96:96,0,177 -chr6 65525121 rs1390272 C T 133.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.271;ClippingRankSum=0.922;DB;DP=16;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.488;POSITIVE_TRAIN_SITE;QD=8.36;ReadPosRankSum=-1.139;SOR=0.412;VQSLOD=5.72;culprit=QD;GENE=EYS GT:AD:DP:GQ:PL 0/1:10,6:16:99:162,0,313 -chr6 65533004 rs34714059 A G 223.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.546;ClippingRankSum=-0.296;DB;DP=10;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.546;POSITIVE_TRAIN_SITE;QD=22.38;ReadPosRankSum=-0.296;SOR=1.609;VQSLOD=5.97;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:3,7:10:91:252,0,91 -chr6 65545787 rs2172886 A G 63.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=7.94;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 65553444 rs2643788 A T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65569554 rs2146756 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65596759 rs7743515 G A 2710.77 PASS AC=2;AF=1.0;AN=2;DB;DP=75;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.59;SOR=2.895;VQSLOD=5.93;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,75:75:99:2739,226,0 -chr6 65611391 rs4710510 T G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65611814 rs57706332 T C 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=7.9;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 65611832 rs142709378 A C 128.03 PASS AC=2;AF=1.0;AN=2;DB;DP=4;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.01;SOR=3.258;VQSLOD=6.74;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,4:4:12:156,12,0 -chr6 65611952 rs59518422 T TATTA 1930.73 PASS AC=2;AF=1.0;AN=2;DB;DP=44;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=50.96;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.09;SOR=3.767;VQSLOD=5.99;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,43:43:99:1968,132,0 -chr6 65612302 rs75634595 A G 3301.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.382;ClippingRankSum=-0.22;DB;DP=215;FS=1.153;MLEAC=1;MLEAF=0.5;MQ=59.83;MQ0=0;MQRankSum=0.451;POSITIVE_TRAIN_SITE;QD=15.36;ReadPosRankSum=2.299;SOR=0.598;VQSLOD=1.86;culprit=DP;GENE=EYS GT:AD:DP:GQ:PL 0/1:108,107:215:99:3330,0,3121 -chr6 65622463 rs9294631 A G 2159.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=4.924;ClippingRankSum=-0.947;DB;DP=134;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.83;MQ0=0;MQRankSum=1.365;POSITIVE_TRAIN_SITE;QD=16.12;ReadPosRankSum=2.546;SOR=0.693;VQSLOD=3.14;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:70,64:134:99:2188,0,2257 -chr6 65622662 rs9445437 G C 2121.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=5.294;ClippingRankSum=0.507;DB;DP=143;FS=5.248;MLEAC=1;MLEAF=0.5;MQ=59.84;MQ0=0;MQRankSum=-0.124;POSITIVE_TRAIN_SITE;QD=14.84;ReadPosRankSum=1.501;SOR=1.441;VQSLOD=1.8;culprit=DP;GENE=EYS GT:AD:DP:GQ:PL 0/1:81,62:143:99:2150,0,2628 -chr6 65622769 rs74484316 A G 456.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.723;ClippingRankSum=-1.231;DB;DP=21;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.336;POSITIVE_TRAIN_SITE;QD=21.75;ReadPosRankSum=1.007;SOR=1.508;VQSLOD=5.31;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:7,14:21:99:485,0,229 -chr6 65622836 rs41516844 C A 40.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=10.19;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=6.04;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:2,2:4:69:69,0,76 -chr6 65632558 rs6455016 T C 256.8 PASS AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=4.174;VQSLOD=6.56;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,7:7:21:285,21,0 -chr6 65678272 rs137904067 C T 28.77 LowQual AC=1;AF=0.5;AN=2;BaseQRankSum=-0.922;ClippingRankSum=-0.922;DB;DP=7;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.922;QD=4.11;ReadPosRankSum=0.922;SOR=0.223;GENE=EYS GT:AD:DP:GQ:PL 0/1:5,2:7:57:57,0,186 -chr6 65715710 . G A 111.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.219;ClippingRankSum=-1.159;DP=9;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.47;MQ0=0;MQRankSum=-0.876;QD=12.42;ReadPosRankSum=-0.361;SOR=0.368;VQSLOD=4.52;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:4,5:9:99:140,0,137 -chr6 65721195 rs7751922 G A 84.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=48.33;MQ0=0;QD=28.09;SOR=2.833;VQSLOD=7.19;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,3:3:9:112,9,0 -chr6 65831684 rs9363336 G A 64.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=1.179;VQSLOD=8.84;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,3:3:9:92,9,0 -chr6 65995024 rs13214404 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65999709 rs6455035 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66005609 rs34666704 AT A 487.73 PASS AC=2;AF=1.0;AN=2;DB;DP=20;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.39;SOR=6.091;VQSLOD=6.41;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,20:20:60:525,60,0 -chr6 66005740 rs35045551 G GA 1585.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.677;ClippingRankSum=-0.71;DB;DP=159;FS=1.564;MLEAC=1;MLEAF=0.5;MQ=59.12;MQ0=0;MQRankSum=0.316;POSITIVE_TRAIN_SITE;QD=9.97;ReadPosRankSum=1.276;SOR=0.921;VQSLOD=1.9;culprit=DP;GENE=EYS GT:AD:DP:GQ:PL 0/1:79,74:153:99:1623,0,1557 -chr6 66005857 rs17411795 T A 4088.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.317;ClippingRankSum=-0.64;DB;DP=271;FS=2.014;MLEAC=1;MLEAF=0.5;MQ=59.57;MQ0=0;MQRankSum=1.167;POSITIVE_TRAIN_SITE;QD=15.09;ReadPosRankSum=2.177;SOR=0.759;VQSLOD=1.94;culprit=DP;GENE=EYS GT:AD:DP:GQ:PL 0/1:136,134:270:99:4117,0,4192 -chr6 66005888 rs9342464 C T 4205.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=8.627;ClippingRankSum=0.069;DB;DP=251;FS=0.459;MLEAC=1;MLEAF=0.5;MQ=59.72;MQ0=0;MQRankSum=0.018;POSITIVE_TRAIN_SITE;QD=16.76;ReadPosRankSum=0.065;SOR=0.647;VQSLOD=1.79;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:126,125:251:99:4234,0,3830 -chr6 66005970 rs9345601 G A 3380.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.543;ClippingRankSum=-0.936;DB;DP=213;FS=2.475;MLEAC=1;MLEAF=0.5;MQ=59.91;MQ0=0;MQRankSum=-1.449;POSITIVE_TRAIN_SITE;QD=15.87;ReadPosRankSum=1.107;SOR=0.516;VQSLOD=1.23;culprit=DP;GENE=EYS GT:AD:DP:GQ:PL 0/1:103,109:212:99:3409,0,3103 -chr6 66006148 rs9342465 A C 503.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.574;ClippingRankSum=0.709;DB;DP=21;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=0.485;POSITIVE_TRAIN_SITE;QD=23.99;ReadPosRankSum=0.485;SOR=1.508;VQSLOD=5.36;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:7,14:21:99:532,0,220 -chr6 66013183 . G A 123.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.273;ClippingRankSum=-0.27;DP=20;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=21.81;MQ0=0;MQRankSum=-0.039;QD=6.19;ReadPosRankSum=0.656;SOR=0.368;VQSLOD=3.44;culprit=QD;GENE=EYS GT:AD:DP:GQ:PL 0/1:12,8:20:99:152,0,259 -chr6 66014572 rs75369872 A G 25.75 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=22.0;MQ0=0;QD=12.88;SOR=2.303;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:53,6,0 -chr6 66018514 rs117228350 A C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=46.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66036758 rs13209408 G A 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.23;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 66045077 rs1502965 C T 2159.77 PASS AC=2;AF=1.0;AN=2;DB;DP=61;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.89;SOR=2.584;VQSLOD=6.42;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,61:61:99:2188,183,0 -chr6 66045118 rs1502964 T C 1434.77 PASS AC=2;AF=1.0;AN=2;DB;DP=42;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.16;SOR=6.091;VQSLOD=6.2;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,42:42:99:1463,126,0 -chr6 66053835 rs1502963 T G 2324.77 PASS AC=2;AF=1.0;AN=2;DB;DP=56;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.46;SOR=6.666;VQSLOD=7.17;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,56:56:99:2353,168,0 -chr6 66063513 rs1936439 G A 3064.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-6.245;ClippingRankSum=-0.619;DB;DP=169;FS=3.043;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.296;POSITIVE_TRAIN_SITE;QD=18.13;ReadPosRankSum=1.339;SOR=0.465;VQSLOD=2.08;culprit=DP;GENE=EYS GT:AD:DP:GQ:PL 0/1:65,104:169:99:3093,0,1991 -chr6 66063766 rs1936440 A C 48.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=16.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.26;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:1,2:3:33:77,0,33 -chr6 66066936 rs9294638 G T 172.9 PASS AC=2;AF=1.0;AN=2;DB;DP=5;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.58;SOR=1.981;VQSLOD=6.69;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,5:5:15:201,15,0 -chr6 66067315 rs976727 A C 49.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=9.3;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 66080074 rs9342469 G C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66112409 rs974110 A G 2596.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-2.384;ClippingRankSum=-0.001;DB;DP=191;FS=0.54;MLEAC=1;MLEAF=0.5;MQ=60.0;MQ0=0;MQRankSum=-1.531;POSITIVE_TRAIN_SITE;QD=13.6;ReadPosRankSum=3.882;SOR=0.763;VQSLOD=1.48;culprit=ReadPosRankSum;GENE=EYS GT:AD:DP:GQ:PL 0/1:102,89:191:99:2625,0,3119 -chr6 66115281 rs34154043 G GAAA 3245.73 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-5.314;ClippingRankSum=1.32;DB;DP=225;FS=0.0;MLEAC=1;MLEAF=0.5;MQ=59.08;MQ0=0;MQRankSum=0.881;POSITIVE_TRAIN_SITE;QD=14.43;ReadPosRankSum=-2.39;SOR=0.705;VQSLOD=1.12;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 0/1:99,90:189:99:3283,0,3862 -chr6 66141229 . T C 20.78 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.39;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:48,6,0 -chr6 66160560 rs9354246 A G 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.68;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 66201364 rs9363379 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66204945 rs12193967 G A 2169.77 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.754;ClippingRankSum=-0.093;DB;DP=128;FS=4.193;MLEAC=1;MLEAF=0.5;MQ=59.82;MQ0=0;MQRankSum=-0.577;POSITIVE_TRAIN_SITE;QD=16.95;ReadPosRankSum=1.481;SOR=0.652;VQSLOD=2.12;culprit=DP;GENE=EYS GT:AD:DP:GQ:PL 0/1:58,70:128:99:2198,0,1773 -chr6 66288101 rs150888347 A AAT 77.25 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.36;MQ0=0;QD=25.75;SOR=1.179;VQSLOD=7.22;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,3:3:9:114,9,0 -chr6 66336763 rs6903740 T C 42.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=2.303;VQSLOD=8.26;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 66336907 rs71736895 CCTTT C 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=5.89;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 66351345 rs6925080 A C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66375671 rs7757773 A T 46.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.43;SOR=1.179;VQSLOD=7.21;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,3:3:9:74,9,0 -chr6 66379893 rs57880191 ACTC A 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.36;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 66379911 rs9283820 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.76;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 66394859 rs1490125 C A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66409784 rs2812776 A G 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.75;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 66409789 rs2814115 T C 62.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.59;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 66411331 rs1490130 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66417384 rs9294647 G T 52.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.92;culprit=FS;GENE=EYS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 66418352 rs1490129 T C 233.8 PASS AC=2;AF=1.0;AN=2;DB;DP=7;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.4;SOR=0.941;VQSLOD=6.77;culprit=FS GT:AD:DP:GQ:PL 1/1:0,7:7:21:262,21,0 -chr6 66418415 rs4609011 T C 54.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.89;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 66456318 rs2636129 T C 49.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=8.31;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 66456442 rs12526256 C T 92.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.76;SOR=1.179;VQSLOD=8.78;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:120,9,0 -chr6 66471880 rs9453396 T G 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66471897 rs9453397 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66471949 rs9445579 C A 53.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=8.8;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 66524243 rs2802047 C T 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66546565 rs4388276 G A 48.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.99;culprit=FS;GENE=ADH5P4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 66547178 rs4392709 G A 7412.77 PASS AC=2;AF=1.0;AN=2;DB;DP=208;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=57.34;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.53;SOR=0.857;VQSLOD=5.34;culprit=QD;GENE=ADH5P4 GT:AD:DP:GQ:PL 1/1:0,208:208:99:7441,625,0 -chr6 66547322 rs9363455 T G 5109.77 PASS AC=2;AF=1.0;AN=2;DB;DP=152;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=53.95;MQ0=0;QD=33.62;SOR=1.319;VQSLOD=4.64;culprit=FS;GENE=ADH5P4 GT:AD:DP:GQ:PL 1/1:0,152:152:99:5138,456,0 -chr6 66568995 rs6931427 G A 62.28 PASS AC=2;AF=1.0;AN=2;DB;DP=3;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 66596125 rs9283821 G A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66610269 rs9363483 A C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66710291 rs1484569 C A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66763069 rs1385225 A G 57.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=9.11;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 66763131 . T A 21.77 LowQual AC=2;AF=1.0;AN=2;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66802808 rs4710310 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66803535 rs2881644 C A 8655.77 PASS AC=2;AF=1.0;AN=2;DB;DP=238;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=59.52;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.36;SOR=0.789;VQSLOD=5.13;culprit=FS;GENE=NUFIP1P GT:AD:DP:GQ:PL 1/1:0,237:237:99:8684,713,0 -chr6 66803769 rs55951409 G GGTTTCT 2785.73 PASS AC=2;AF=1.0;AN=2;DB;DP=59;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=31.86;MQ0=0;QD=27.53;SOR=0.96;VQSLOD=4.58;culprit=FS;GENE=NUFIP1P GT:AD:DP:GQ:PL 1/1:0,57:57:99:2823,189,0 -chr6 66804609 rs147166458 GACTC G 322.75 PASS AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=45.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.87;SOR=1.179;VQSLOD=5.97;culprit=FS;GENE=NUFIP1P GT:AD:DP:GQ:PL 1/1:0,8:8:24:360,24,0 -chr6 66804622 rs3925325 G C 368.78 PASS AC=2;AF=1.0;AN=2;DB;DP=8;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=49.49;MQ0=0;QD=30.3;SOR=1.179;VQSLOD=5.58;culprit=FS;GENE=NUFIP1P GT:AD:DP:GQ:PL 1/1:0,8:8:27:397,27,0 -chr6 66804958 rs3030466 C CCT 52.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.35;SOR=2.303;VQSLOD=8.57;culprit=FS;GENE=NUFIP1P GT:AD:DP:GQ:PL 1/1:0,2:2:6:89,6,0 -chr6 66807446 rs7738469 T C 53.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=26.87;SOR=2.303;VQSLOD=7.44;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 66818604 rs3846808 T C 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66829961 rs11287287 AG A 38.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=0.693;VQSLOD=8.71;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 66836869 rs13217074 A G 56.74 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=7.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 66849936 rs866452 T A 21.77 LowQual AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66871532 rs138893096 C CAAAG 53.7 PASS AC=2;AF=1.0;AN=2;DB;DP=2;FS=0.0;MLEAC=2;MLEAF=1.0;MQ=60.0;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=8.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 diff --git a/run.py b/run.py deleted file mode 100755 index d52e909..0000000 --- a/run.py +++ /dev/null @@ -1,46 +0,0 @@ -#!/usr/bin/env python -import argparse -import json -import logging -import sys - -from variantapi.client import VariantAPIClient - -__author__ = 'ckopanos' -logging.basicConfig(level=logging.DEBUG, - format='[%(levelname)s] %(threadName)s %(message)s', - ) - - -def main(argv): - parser = argparse.ArgumentParser(description='Sample Variant API calls') - parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=False) - parser.add_argument('-g', help='Reference genome either hg19 or hg38', type=str, metavar='Reference Genome', - required=False, default='hg19') - parser.add_argument('-q', - help='Query to lookup in the API e.g. chr19:20082943:1:G or in case of batch request ' - 'e.g. chr19:20082943:1:G rs113488022', - type=str, metavar='Query', required=True, nargs='+') - parser.add_argument('-p', - help='Request parameters e.g. add-all-data=1 expand-pubmed-articles=0', - type=str, metavar='Request Params', required=False, nargs='+') - args = parser.parse_args() - api_key = args.k - query = args.q - ref_genome = args.g - request_parameters = None - if args.p: - request_parameters = {param[0]: param[1] for param in [param.split("=") for param in args.p]} - api = VariantAPIClient(api_key) - if len(query) == 1: - result = api.lookup(query[0], params=request_parameters, ref_genome=ref_genome) - else: - if api_key is None: - sys.exit("You need to pass an api key to perform batch requests") - result = api.batch_lookup(query, params=request_parameters, ref_genome=ref_genome) - sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result") - sys.stdout.write("\n") - - -if __name__ == "__main__": - main(sys.argv[1:]) diff --git a/sample.vcf b/sample.vcf deleted file mode 100644 index 94cd3d1..0000000 --- a/sample.vcf +++ /dev/null @@ -1,2132 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##GATKCommandLine= -##GATKCommandLine= -##GATKCommandLine= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##reference=file:///ref/genomes/hg19/hg19.fa -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR309291 -chr6 44387517 rs6923521 C G 184.84 PASS AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.81;SOR=3.912;VQSLOD=6.47;culprit=FS GT:AD:DP:GQ:PL 1/1:0,6:6:18:213,18,0 -chr6 44410746 rs61581947 GT G 17.78 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=5.93;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:54,6,0 -chr6 44453701 rs60176543 G A 15.65 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=7.83;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0 -chr6 44505655 rs9296442 G T 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 -chr6 44526440 rs991234 A C 36.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.37;SOR=0.693;VQSLOD=7.54;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:64,6,0 -chr6 44532454 rs76750540 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44547060 rs67452991 C T 102.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.51;SOR=0.693;VQSLOD=5.66;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:130,12,0 -chr6 44562107 rs491616 G C 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:28:40,0,28 -chr6 44575012 rs636287 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44584484 rs634631 A T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44585311 rs648579 T C 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.91;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 44586011 rs651831 G C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44586363 rs6913259 C T 171.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.38;SOR=3.611;VQSLOD=6.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:200,15,0 -chr6 44595393 rs1767788 C T 53.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=9.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 44605066 rs6934182 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44605461 rs4714809 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44629576 rs4257850 A G 60.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=2.303;VQSLOD=9.47;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:88,6,0 -chr6 44635852 rs4711794 C A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44640206 rs527082 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44775098 . C A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44780682 rs622923 G T 14.68 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=7.34;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:41,3,0 -chr6 44780701 rs559322 C T 15.65 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=7.83;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0 -chr6 44781313 rs5875893 G GA 15.82 LowQual AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=3.95;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:52,6,0 -chr6 44797271 rs9369514 C A 241.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.54;SOR=2.584;VQSLOD=6.76;culprit=FS GT:AD:DP:GQ:PL 1/1:0,7:7:21:270,21,0 -chr6 44825715 rs9395051 C A 71.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.76;SOR=0.693;VQSLOD=7.41;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 -chr6 44834094 rs3846896 G A 15.65 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=7.83;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0 -chr6 44840376 rs1293588 A C 40.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=20.37;SOR=2.303;VQSLOD=6.79;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 44888740 rs608941 C T 94.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=1.179;VQSLOD=8.87;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:122,9,0 -chr6 44899632 rs679713 T C 1144.77 PASS AC=2;AF=1.00;AN=2;DB;DP=27;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.54;SOR=6.666;VQSLOD=6.85;culprit=FS GT:AD:DP:GQ:PL 1/1:0,27:27:81:1173,81,0 -chr6 44900253 rs3799986 A G 188.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.64;SOR=3.611;VQSLOD=6.39;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:217,15,0 -chr6 44903248 rs10948186 C T 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=2.303;VQSLOD=8.97;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 44921320 rs10948187 C T 89.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.76;SOR=2.833;VQSLOD=8.75;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:117,9,0 -chr6 44921962 rs625782 T C 65.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.76;SOR=2.833;VQSLOD=7.90;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:93,9,0 -chr6 44935341 rs636845 C T 60.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.09;SOR=1.179;VQSLOD=8.15;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:88,9,0 -chr6 44952716 rs5875900 GT G 29.71 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=14.85;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:66,6,0 -chr6 44972729 rs1159132 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 44988149 rs1475534 C T 529.77 PASS AC=2;AF=1.00;AN=2;DB;DP=14;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.74;SOR=5.421;VQSLOD=7.17;culprit=FS GT:AD:DP:GQ:PL 1/1:0,14:14:42:558,42,0 -chr6 45003928 rs4398713 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45020697 rs2149872 A G 61.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.40;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 -chr6 45066168 rs150556986 G A 167.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.388;ClippingRankSum=0.194;DB;DP=14;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.194;POSITIVE_TRAIN_SITE;QD=11.98;ReadPosRankSum=-0.968;SOR=1.402;VQSLOD=5.50;culprit=FS GT:AD:DP:GQ:PL 0/1:8,6:14:99:196,0,294 -chr6 45073967 rs2396381 A G 88.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.43;SOR=2.833;VQSLOD=8.42;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:116,9,0 -chr6 45090876 . T C 19.79 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=9.89;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:47,6,0 -chr6 45159414 rs11321900 TA T 24.72 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=12.36;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 -chr6 45163350 rs1748242 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45170121 rs1284955 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45175908 rs9381373 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45177025 rs2396425 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45192941 rs6911320 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45203918 rs6937317 T C 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.23;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 45268574 rs111541141 T TAAGAC 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.28;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 45360194 rs9395099 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45390962 rs11498196 C T 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=7.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 45444061 rs2677110 C T 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=9.10;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 45444083 rs35663521 G GA 38.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=0.693;VQSLOD=7.75;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 45456564 rs12215249 G T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45486207 rs7771889 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45511541 rs10948238 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45519443 . A G 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45521733 rs1201807 C T 47.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=2.303;VQSLOD=8.89;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 45521847 rs70996341 ATGTG A 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=5.79;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 45523928 rs675613 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45523947 rs5875926 G GA 24.72 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=12.36;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 -chr6 45564510 rs713270 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45609347 . G GT 22.73 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=11.36;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:59,6,0 -chr6 45705659 rs829913 T A 96.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.09;SOR=1.179;VQSLOD=7.64;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:124,9,0 -chr6 45733276 rs6942337 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45749983 rs9357491 A G 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.52;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 45754997 rs1037281 A C 50.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=0.693;VQSLOD=9.52;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 45764956 rs11276783 ACAGGGCAGCT A 98.25 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.75;SOR=2.833;VQSLOD=7.83;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 45769869 rs10948257 G A 49.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=7.93;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 45792170 rs12197564 G T 13.72 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=6.86;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 -chr6 45808216 . C A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45833836 rs142466444 TTTTC T 85.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=-0.727;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;POSITIVE_TRAIN_SITE;QD=17.15;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=6.32;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:43:123,0,43 -chr6 45847678 rs2396559 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45851886 rs1932042 C T 61.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.58;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 -chr6 45858548 rs71566550 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45870999 rs35735653 CAG C 269.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.065;ClippingRankSum=0.457;DB;DP=33;FS=4.212;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-1.588;POSITIVE_TRAIN_SITE;QD=8.17;ReadPosRankSum=0.239;SOR=1.802;VQSLOD=2.22;culprit=FS GT:AD:DP:GQ:PL 0/1:22,9:31:99:307,0,882 -chr6 45888576 rs34155361 ATGC A 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.66;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 45893031 rs6939554 C T 35.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.87;SOR=0.693;VQSLOD=7.73;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:63,6,0 -chr6 45901916 rs9349337 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45909139 rs11421773 C CG 234.74 PASS AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.08;SOR=2.833;VQSLOD=6.34;culprit=FS GT:AD:DP:GQ:PL 1/1:0,8:8:27:272,27,0 -chr6 45914028 rs3777582 A T 13.72 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=13.72;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 -chr6 45915413 rs1890368 C G 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.11;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 45915504 rs1890369 A C 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.66;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 45919719 rs3777587 A G 60.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=2.303;VQSLOD=6.51;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:88,6,0 -chr6 45919758 rs3777588 G A 120.78 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.731;ClippingRankSum=-0.731;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.731;POSITIVE_TRAIN_SITE;QD=24.16;ReadPosRankSum=0.731;SOR=1.981;VQSLOD=6.26;culprit=FS GT:AD:DP:GQ:PL 0/1:1,4:5:27:149,0,27 -chr6 45921108 rs3777590 G C 63.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=9.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 45922849 rs3734206 C T 1890.77 PASS AC=2;AF=1.00;AN=2;DB;DP=48;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.58;SOR=6.316;VQSLOD=6.34;culprit=QD GT:AD:DP:GQ:PL 1/1:0,47:47:99:1919,141,0 -chr6 45923126 rs6909306 A C 252.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.60;SOR=4.407;VQSLOD=6.96;culprit=FS GT:AD:DP:GQ:PL 1/1:0,8:8:24:281,24,0 -chr6 45965608 rs3777612 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45989366 rs1204338 A C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 45994992 rs1547605 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46025834 rs1535110 T G 23.58 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=7.86;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:7:51,7,0 -chr6 46047269 rs9381423 T C 124.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.945;ClippingRankSum=0.453;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=-1.586;POSITIVE_TRAIN_SITE;QD=7.80;ReadPosRankSum=1.586;SOR=0.223;VQSLOD=4.04;culprit=QD GT:AD:DP:GQ:PL 0/1:11,5:16:99:153,0,375 -chr6 46047458 rs3734207 C T 3075.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-7.190;ClippingRankSum=-0.231;DB;DP=213;FS=0.542;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=-1.583;POSITIVE_TRAIN_SITE;QD=14.44;ReadPosRankSum=0.457;SOR=0.754;VQSLOD=1.68;culprit=FS GT:AD:DP:GQ:PL 0/1:107,105:212:99:3104,0,3533 -chr6 46048000 rs1416165 T C 2778.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.171;ClippingRankSum=0.218;DB;DP=172;FS=0.639;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.131;POSITIVE_TRAIN_SITE;QD=16.16;ReadPosRankSum=-1.044;SOR=0.794;VQSLOD=1.61;culprit=FS GT:AD:DP:GQ:PL 0/1:74,98:172:99:2807,0,2169 -chr6 46107115 rs61381984 A AT 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=4;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=3.01;ReadPosRankSum=0.736;SOR=2.225 GT:AD:DP:GQ:PL 0/1:1,2:3:20:49,0,20 -chr6 46107312 rs11752816 G A 1890.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.790;ClippingRankSum=0.077;DB;DP=125;FS=3.508;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.580;POSITIVE_TRAIN_SITE;QD=15.13;ReadPosRankSum=-1.351;SOR=0.335;VQSLOD=2.14;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:62,63:125:99:1919,0,1762 -chr6 46107752 rs7451713 C G 5119.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=7.032;ClippingRankSum=-2.826;DB;DP=301;FS=1.419;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=-0.805;POSITIVE_TRAIN_SITE;QD=17.01;ReadPosRankSum=0.708;SOR=0.792;VQSLOD=1.55;culprit=DP GT:AD:DP:GQ:PL 0/1:146,155:301:99:5148,0,4240 -chr6 46110821 rs7769902 A G 202.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.085;ClippingRankSum=0.380;DB;DP=19;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=-0.211;POSITIVE_TRAIN_SITE;QD=10.67;ReadPosRankSum=-0.549;SOR=0.321;VQSLOD=4.71;culprit=FS GT:AD:DP:GQ:PL 0/1:12,7:19:99:231,0,378 -chr6 46110844 rs35942390 T TGA 174.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;ClippingRankSum=-0.444;DB;DP=27;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.95;MQ0=0;MQRankSum=1.467;POSITIVE_TRAIN_SITE;QD=6.47;ReadPosRankSum=-0.853;SOR=0.307;VQSLOD=5.69;culprit=FS GT:AD:DP:GQ:PL 0/1:14,8:22:99:212,0,429 -chr6 46124799 rs9367237 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46129345 rs2235881 G A 4707.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=6.532;ClippingRankSum=-0.307;DB;DP=317;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=0.655;POSITIVE_TRAIN_SITE;QD=14.85;ReadPosRankSum=2.066;SOR=0.698;VQSLOD=1.89;culprit=FS GT:AD:DP:GQ:PL 0/1:162,154:316:99:4736,0,4689 -chr6 46135489 rs6926570 T C 3065.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=6.245;ClippingRankSum=0.018;DB;DP=187;FS=1.135;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=0.009;POSITIVE_TRAIN_SITE;QD=16.39;ReadPosRankSum=1.610;SOR=0.809;VQSLOD=2.66;culprit=DP GT:AD:DP:GQ:PL 0/1:96,91:187:99:3094,0,2997 -chr6 46135984 rs3806995 G T 1685.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.855;ClippingRankSum=-0.003;DB;DP=117;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.406;POSITIVE_TRAIN_SITE;QD=14.41;ReadPosRankSum=2.665;SOR=0.727;VQSLOD=4.05;culprit=FS GT:AD:DP:GQ:PL 0/1:61,56:117:99:1714,0,1985 -chr6 46148778 rs34512199 AT A 24.72 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=12.36;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 -chr6 46170924 . G T 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46206776 rs55832349 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46219283 rs6910477 G A 47.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=2.303;VQSLOD=8.19;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 46259017 rs11389800 G GT 13.89 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=63.51;MQ0=0;QD=4.63;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:50,6,0 -chr6 46293328 rs2277121 G A 717.77 PASS AC=2;AF=1.00;AN=2;DB;DP=19;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.88;SOR=5.994;VQSLOD=6.73;culprit=FS GT:AD:DP:GQ:PL 1/1:0,19:19:57:746,57,0 -chr6 46296710 rs6906742 C T 62.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.44;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 46302975 rs60870663 T A 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.40;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 46302987 rs58585138 A G 46.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.37;SOR=2.303;VQSLOD=7.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:74,6,0 -chr6 46312875 rs9367242 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46321514 . T C 20.78 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.39;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:48,6,0 -chr6 46326865 . C G 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46456536 rs9349362 C T 33.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=11.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=5.66;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:34:62,0,34 -chr6 46462514 . C A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46469927 rs59470467 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46470622 rs67200907 G A 48.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.76;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 46479322 rs1609661 A G 63.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.22;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 46490097 rs4714943 C A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46512200 . T C 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46521602 rs699939 C A 599.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.640;ClippingRankSum=0.714;DB;DP=46;FS=1.296;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-0.647;POSITIVE_TRAIN_SITE;QD=13.04;ReadPosRankSum=2.186;SOR=0.911;VQSLOD=2.11;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:27,19:46:99:628,0,724 -chr6 46563817 rs7761731 A T 3102.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.173;ClippingRankSum=-1.345;DB;DP=194;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=0.519;POSITIVE_TRAIN_SITE;QD=15.99;ReadPosRankSum=0.699;SOR=0.739;VQSLOD=2.35;culprit=FS GT:AD:DP:GQ:PL 0/1:90,104:194:99:3131,0,2802 -chr6 46607081 rs3085602 AT A 645.73 PASS AC=2;AF=1.00;AN=2;DB;DP=20;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.29;SOR=6.091;VQSLOD=5.95;culprit=FS GT:AD:DP:GQ:PL 1/1:0,20:20:60:683,60,0 -chr6 46620252 rs12192544 C G 5715.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=2.691;ClippingRankSum=0.485;DB;DP=440;FS=1.133;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=-2.934;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=12.99;ReadPosRankSum=-0.818;SOR=0.805;VQSLOD=-9.355e-01;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:239,200:439:99:5744,0,6851 -chr6 46623698 rs3757241 T C 6720.77 PASS AC=2;AF=1.00;AN=2;DB;DP=183;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.06;SOR=0.822;VQSLOD=5.03;culprit=FS GT:AD:DP:GQ:PL 1/1:0,179:179:99:6749,538,0 -chr6 46625274 rs9381468 A G 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=9.35;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 46626353 rs953062 A G 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.60;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 46630068 rs9381469 G A 907.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.991;ClippingRankSum=-0.318;DB;DP=68;FS=14.136;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.231;POSITIVE_TRAIN_SITE;QD=13.35;ReadPosRankSum=1.115;SOR=3.003;VQSLOD=1.21;culprit=FS GT:AD:DP:GQ:PL 0/1:40,28:68:99:936,0,1206 -chr6 46637908 rs200254015 A C 76.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-5.158;ClippingRankSum=-1.074;DB;DP=72;FS=148.770;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=-0.756;QD=1.07;ReadPosRankSum=-5.463;SOR=5.781;VQSLOD=-4.745e+01;culprit=FS GT:AD:DP:GQ:PL 0/1:55,17:72:99:105,0,1883 -chr6 46649231 rs7740677 C T 6652.77 PASS AC=2;AF=1.00;AN=2;DB;DP=183;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.24;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.56;SOR=2.067;VQSLOD=5.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,183:183:99:6681,550,0 -chr6 46657057 rs3799277 A G 4300.77 PASS AC=2;AF=1.00;AN=2;DB;DP=112;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.78;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.29;SOR=1.350;VQSLOD=6.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,111:111:99:4329,334,0 -chr6 46658905 rs9381472 C G 2370.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.957;ClippingRankSum=-1.243;DB;DP=147;FS=3.996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.165;POSITIVE_TRAIN_SITE;QD=16.13;ReadPosRankSum=0.979;SOR=1.036;VQSLOD=2.15;culprit=DP GT:AD:DP:GQ:PL 0/1:77,70:147:99:2399,0,2735 -chr6 46661937 rs55724083 CT C 307.76 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.021;ClippingRankSum=0.615;DB;DP=81;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.11;MQ0=0;MQRankSum=-0.913;POSITIVE_TRAIN_SITE;QD=3.80;ReadPosRankSum=0.542;SOR=3.026;VQSLOD=5.76;culprit=FS GT:AD:DP:GQ:PL 0/1:6,30:36:22:345,0,22 -chr6 46672205 . TCTCTCTCTCTCA T 62.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.219;ClippingRankSum=0.361;DP=48;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.85;MQ0=0;MQRankSum=-1.307;QD=1.31;ReadPosRankSum=2.219;SOR=0.892;VQSLOD=2.56;culprit=FS GT:AD:DP:GQ:PL 0/1:15,5:20:99:100,0,440 -chr6 46672452 rs148052037 TAATC T 1973.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.650;ClippingRankSum=1.355;DB;DP=107;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.10;MQ0=0;MQRankSum=-2.444;POSITIVE_TRAIN_SITE;QD=18.45;ReadPosRankSum=-0.854;SOR=0.718;VQSLOD=3.96;culprit=FS GT:AD:DP:GQ:PL 0/1:51,52:103:99:2011,0,3030 -chr6 46672943 rs1051931 A G 6548.77 PASS AC=2;AF=1.00;AN=2;DB;DP=172;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.65;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.43;SOR=1.172;VQSLOD=3.94;culprit=FS GT:AD:DP:GQ:PL 1/1:0,170:170:99:6577,511,0 -chr6 46676019 rs2216465 C G 430.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.311;ClippingRankSum=0.241;DB;DP=29;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.548;POSITIVE_TRAIN_SITE;QD=14.85;ReadPosRankSum=-0.022;SOR=0.518;VQSLOD=5.37;culprit=FS GT:AD:DP:GQ:PL 0/1:16,13:29:99:459,0,615 -chr6 46682079 rs1362931 A C 1919.77 PASS AC=2;AF=1.00;AN=2;DB;DP=50;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.23;SOR=7.864;VQSLOD=7.44;culprit=FS GT:AD:DP:GQ:PL 1/1:0,50:50:99:1948,150,0 -chr6 46683978 rs41361844 T TA 363.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.549;ClippingRankSum=1.214;DB;DP=33;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.33;MQ0=0;MQRankSum=-0.419;POSITIVE_TRAIN_SITE;QD=11.02;ReadPosRankSum=1.046;SOR=0.473;VQSLOD=6.00;culprit=FS GT:AD:DP:GQ:PL 0/1:17,13:30:99:401,0,436 -chr6 46684222 rs1805017 C T 2595.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.964;ClippingRankSum=-0.355;DB;DP=171;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=1.275;POSITIVE_TRAIN_SITE;QD=15.18;ReadPosRankSum=0.601;SOR=0.648;VQSLOD=2.60;culprit=FS GT:AD:DP:GQ:PL 0/1:85,85:170:99:2624,0,2396 -chr6 46685286 rs6929105 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46689762 rs9472830 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46695144 . G A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46714081 rs141667902 GTTCTCC G 187.87 PASS AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.03;MQ0=0;QD=31.31;SOR=1.022;VQSLOD=5.89;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:225,15,0 -chr6 46727772 rs6918050 G C 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.87;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 46730039 . A G 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=27.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46761495 rs2274656 G A 1258.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.705;ClippingRankSum=0.492;DB;DP=66;FS=11.133;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.161;POSITIVE_TRAIN_SITE;QD=19.07;ReadPosRankSum=0.794;SOR=0.077;VQSLOD=0.934;culprit=FS GT:AD:DP:GQ:PL 0/1:26,40:66:99:1287,0,859 -chr6 46766467 rs872018 G C 826.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.434;ClippingRankSum=0.387;DB;DP=45;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.49;MQ0=0;MQRankSum=0.716;POSITIVE_TRAIN_SITE;QD=18.37;ReadPosRankSum=-3.462;SOR=1.681;VQSLOD=3.22;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:22,22:44:99:855,0,1647 -chr6 46766468 rs872019 G C 826.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.555;ClippingRankSum=-0.670;DB;DP=46;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=-0.329;POSITIVE_TRAIN_SITE;QD=17.97;ReadPosRankSum=-2.986;SOR=1.609;VQSLOD=4.20;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:23,22:45:99:855,0,1647 -chr6 46775361 rs2894714 A G 95.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.76;SOR=1.179;VQSLOD=6.48;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:123,9,0 -chr6 46777377 rs1833460 T C 2742.77 PASS AC=2;AF=1.00;AN=2;DB;DP=78;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.70;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.37;SOR=5.892;VQSLOD=6.63;culprit=FS GT:AD:DP:GQ:PL 1/1:0,78:78:99:2771,235,0 -chr6 46784183 rs9367257 A G 59.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.03;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 46793175 rs6920863 G A 976.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.347;ClippingRankSum=0.690;DB;DP=69;FS=2.675;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.762;POSITIVE_TRAIN_SITE;QD=14.16;ReadPosRankSum=-0.654;SOR=0.378;VQSLOD=3.19;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:35,34:69:99:1005,0,1233 -chr6 46794048 rs2297018 C G 1559.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.778;ClippingRankSum=1.150;DB;DP=86;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=0.527;POSITIVE_TRAIN_SITE;QD=18.14;ReadPosRankSum=-0.821;SOR=0.791;VQSLOD=4.49;culprit=FS GT:AD:DP:GQ:PL 0/1:41,45:86:99:1588,0,1376 -chr6 46797329 rs2274657 G A 1320.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.675;ClippingRankSum=0.827;DB;DP=98;FS=1.251;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=0;MQRankSum=-0.371;POSITIVE_TRAIN_SITE;QD=13.48;ReadPosRankSum=0.307;SOR=0.399;VQSLOD=3.23;culprit=DP GT:AD:DP:GQ:PL 0/1:53,45:98:99:1349,0,1847 -chr6 46797515 rs6903045 G A 68.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.406;ClippingRankSum=0.406;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.406;POSITIVE_TRAIN_SITE;QD=11.46;ReadPosRankSum=0.406;SOR=2.093;VQSLOD=6.66;culprit=FS GT:AD:DP:GQ:PL 0/1:3,3:6:73:97,0,73 -chr6 46801071 rs2274658 G T 2458.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.720;ClippingRankSum=0.231;DB;DP=169;FS=2.721;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.436;POSITIVE_TRAIN_SITE;QD=14.55;ReadPosRankSum=2.140;SOR=0.917;VQSLOD=2.52;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:89,80:169:99:2487,0,2786 -chr6 46802172 . ATATTTATT A 98.25 PASS AC=2;AF=1.00;AN=2;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=32.75;SOR=2.833;VQSLOD=6.56;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 46802370 rs4714952 G A 4383.77 PASS AC=2;AF=1.00;AN=2;DB;DP=119;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.22;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.86;SOR=1.198;VQSLOD=7.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,119:119:99:4412,357,0 -chr6 46802901 rs2297021 G C 87.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.720;ClippingRankSum=0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=0.720;POSITIVE_TRAIN_SITE;QD=14.63;ReadPosRankSum=-0.720;SOR=0.368;VQSLOD=5.79;culprit=FS GT:AD:DP:GQ:PL 0/1:2,4:6:67:116,0,67 -chr6 46803018 rs2297020 A T 292.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.746;ClippingRankSum=0.040;DB;DP=32;FS=3.467;MLEAC=1;MLEAF=0.500;MQ=58.35;MQ0=0;MQRankSum=0.913;POSITIVE_TRAIN_SITE;QD=9.15;ReadPosRankSum=-0.357;SOR=1.659;VQSLOD=2.47;culprit=QD GT:AD:DP:GQ:PL 0/1:21,11:32:99:321,0,590 -chr6 46803102 rs2297019 A G 273.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.297;ClippingRankSum=-1.681;DB;DP=23;FS=1.740;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=-1.484;POSITIVE_TRAIN_SITE;QD=11.90;ReadPosRankSum=-0.495;SOR=0.925;VQSLOD=2.16;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:12,10:22:99:302,0,349 -chr6 46803345 rs12196017 G A 98.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.754;ClippingRankSum=0.550;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.07;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=14.11;ReadPosRankSum=1.754;SOR=0.941;VQSLOD=6.35;culprit=FS GT:AD:DP:GQ:PL 0/1:3,4:7:96:127,0,96 -chr6 46806766 rs115391170 G A 1395.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.528;ClippingRankSum=0.481;DB;DP=95;FS=14.804;MLEAC=1;MLEAF=0.500;MQ=56.80;MQ0=0;MQRankSum=2.724;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=14.69;ReadPosRankSum=1.677;SOR=0.144;VQSLOD=-1.508e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:44,48:92:99:1424,0,1271 -chr6 46806802 rs143826629 G A 1031.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.214;ClippingRankSum=0.523;DB;DP=71;FS=2.497;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=0.719;QD=14.53;ReadPosRankSum=-0.144;SOR=0.401;VQSLOD=1.61;culprit=DP GT:AD:DP:GQ:PL 0/1:36,35:71:99:1060,0,1434 -chr6 46806809 rs1804211 C T 1130.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.852;ClippingRankSum=0.535;DB;DP=71;FS=1.182;MLEAC=1;MLEAF=0.500;MQ=55.98;MQ0=0;MQRankSum=-0.121;POSITIVE_TRAIN_SITE;QD=15.93;ReadPosRankSum=1.122;SOR=0.995;VQSLOD=3.20;culprit=FS GT:AD:DP:GQ:PL 0/1:34,37:71:99:1159,0,1325 -chr6 46806939 rs17468190 G T 181.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.380;ClippingRankSum=0.244;DB;DP=14;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=46.24;MQ0=0;MQRankSum=-1.977;POSITIVE_TRAIN_SITE;QD=12.98;ReadPosRankSum=0.689;SOR=1.022;VQSLOD=4.95;culprit=FS GT:AD:DP:GQ:PL 0/1:5,7:12:99:210,0,155 -chr6 46806948 rs150225810 G GTTTGGGGCAGCT 230.82 PASS AC=2;AF=1.00;AN=2;DB;DP=12;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.62;MQ0=0;QD=19.23;SOR=3.912;VQSLOD=4.37;culprit=FS GT:AD:DP:GQ:PL 1/1:0,6:6:17:268,17,0 -chr6 46807040 rs1059276 C A 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 46817550 rs6929917 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46817982 rs6458525 C T 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.65;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 46821191 . A G 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:28:40,0,28 -chr6 46822349 rs475991 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46823695 rs657340 G A 1861.77 PASS AC=2;AF=1.00;AN=2;DB;DP=53;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.56;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.21;SOR=1.893;VQSLOD=6.39;culprit=FS GT:AD:DP:GQ:PL 1/1:0,52:52:99:1890,156,0 -chr6 46823805 rs58687946 A AG 1627.73 PASS AC=2;AF=1.00;AN=2;DB;DP=50;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.74;MQ0=0;QD=32.55;SOR=2.511;VQSLOD=4.68;culprit=FS GT:AD:DP:GQ:PL 1/1:0,46:46:99:1665,138,0 -chr6 46824279 rs526123 A G 176.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.248;ClippingRankSum=1.203;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.96;MQ0=0;MQRankSum=-1.683;POSITIVE_TRAIN_SITE;QD=19.64;ReadPosRankSum=-0.573;SOR=1.402;VQSLOD=5.29;culprit=FS GT:AD:DP:GQ:PL 0/1:3,6:9:92:205,0,92 -chr6 46824448 rs643409 A G 2848.77 PASS AC=2;AF=1.00;AN=2;DB;DP=83;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.32;SOR=1.816;VQSLOD=7.31;culprit=FS GT:AD:DP:GQ:PL 1/1:0,83:83:99:2877,250,0 -chr6 46824798 rs521502 C G 420.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.32;SOR=4.977;VQSLOD=6.96;culprit=FS GT:AD:DP:GQ:PL 1/1:0,11:11:33:449,33,0 -chr6 46825595 rs2281443 G A 37.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.87;SOR=2.303;VQSLOD=8.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:65,6,0 -chr6 46825632 rs627910 G C 40.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.37;SOR=2.303;VQSLOD=7.74;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 46826508 rs613870 G A 2427.77 PASS AC=2;AF=1.00;AN=2;DB;DP=67;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.42;SOR=0.917;VQSLOD=7.01;culprit=DP GT:AD:DP:GQ:PL 1/1:0,67:67:99:2456,202,0 -chr6 46826715 rs572248 T A 4133.77 PASS AC=2;AF=1.00;AN=2;DB;DP=118;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.35;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.43;SOR=0.881;VQSLOD=6.50;culprit=FS GT:AD:DP:GQ:PL 1/1:0,114:114:99:4162,343,0 -chr6 46826844 rs571247 T C 5230.77 PASS AC=2;AF=1.00;AN=2;DB;DP=144;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.63;SOR=1.006;VQSLOD=6.93;culprit=FS GT:AD:DP:GQ:PL 1/1:0,144:144:99:5259,433,0 -chr6 46826910 rs611779 G A 4855.77 PASS AC=2;AF=1.00;AN=2;DB;DP=132;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.04;SOR=1.119;VQSLOD=5.95;culprit=FS GT:AD:DP:GQ:PL 1/1:0,132:132:99:4884,397,0 -chr6 46826979 rs9381487 A G 1623.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.727;ClippingRankSum=-0.199;DB;DP=106;FS=2.830;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.130;POSITIVE_TRAIN_SITE;QD=15.32;ReadPosRankSum=0.117;SOR=1.041;VQSLOD=2.59;culprit=DP GT:AD:DP:GQ:PL 0/1:54,52:106:99:1652,0,1669 -chr6 46827073 rs547499 A G 1003.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.612;ClippingRankSum=-0.887;DB;DP=64;FS=0.955;MLEAC=1;MLEAF=0.500;MQ=58.48;MQ0=0;MQRankSum=-0.699;POSITIVE_TRAIN_SITE;QD=15.68;ReadPosRankSum=-0.094;SOR=0.831;VQSLOD=2.97;culprit=FS GT:AD:DP:GQ:PL 0/1:31,33:64:99:1032,0,968 -chr6 46827126 rs610856 C T 2450.77 PASS AC=2;AF=1.00;AN=2;DB;DP=64;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.18;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.98;SOR=0.966;VQSLOD=5.61;culprit=FS GT:AD:DP:GQ:PL 1/1:0,64:64:99:2479,192,0 -chr6 46827239 rs9395218 C T 1247.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.769;ClippingRankSum=-0.087;DB;DP=83;FS=13.228;MLEAC=1;MLEAF=0.500;MQ=51.70;MQ0=0;MQRankSum=0.844;POSITIVE_TRAIN_SITE;QD=15.03;ReadPosRankSum=1.346;SOR=0.158;VQSLOD=1.45;culprit=FS GT:AD:DP:GQ:PL 0/1:39,44:83:99:1276,0,1186 -chr6 46828670 rs540727 A G 1780.77 PASS AC=2;AF=1.00;AN=2;DB;DP=46;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.96;SOR=4.804;VQSLOD=6.53;culprit=FS GT:AD:DP:GQ:PL 1/1:0,46:46:99:1809,138,0 -chr6 46830243 rs483813 T C 95.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=1.179;VQSLOD=8.22;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:123,9,0 -chr6 46832536 rs531049 T C 161.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.96;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.38;SOR=3.611;VQSLOD=6.60;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:190,15,0 -chr6 46832553 rs530990 A G 80.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.76;SOR=2.833;VQSLOD=8.23;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:108,9,0 -chr6 46832642 rs615677 A C 985.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.43;SOR=6.593;VQSLOD=7.43;culprit=FS GT:AD:DP:GQ:PL 1/1:0,26:26:78:1014,78,0 -chr6 46832741 rs529201 T C 4511.77 PASS AC=2;AF=1.00;AN=2;DB;DP=123;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.85;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.57;SOR=3.352;VQSLOD=5.31;culprit=FS GT:AD:DP:GQ:PL 1/1:0,123:123:99:4540,368,0 -chr6 46832813 rs614826 G A 3006.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-7.723;ClippingRankSum=-0.748;DB;DP=234;FS=8.321;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=1.246;POSITIVE_TRAIN_SITE;QD=12.85;ReadPosRankSum=1.650;SOR=1.157;VQSLOD=1.43;culprit=FS GT:AD:DP:GQ:PL 0/1:127,107:234:99:3035,0,4266 -chr6 46834473 rs586986 T G 189.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.86;SOR=3.611;VQSLOD=5.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:218,15,0 -chr6 46834685 rs586024 G A 4443.77 PASS AC=2;AF=1.00;AN=2;DB;DP=121;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.50;SOR=1.857;VQSLOD=6.18;culprit=FS GT:AD:DP:GQ:PL 1/1:0,121:121:99:4472,364,0 -chr6 46834906 rs5875987 TG T 2501.73 PASS AC=2;AF=1.00;AN=2;DB;DP=69;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.62;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.68;SOR=3.007;VQSLOD=5.93;culprit=FS GT:AD:DP:GQ:PL 1/1:0,68:68:99:2539,205,0 -chr6 46836406 rs665551 G C 117.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.26;SOR=3.258;VQSLOD=5.89;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:145,12,0 -chr6 46836995 rs515866 T C 146.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.38;SOR=3.611;VQSLOD=6.79;culprit=DP GT:AD:DP:GQ:PL 1/1:0,5:5:15:175,15,0 -chr6 46839435 rs58989382 T C 406.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.854;ClippingRankSum=-0.174;DB;DP=24;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.927;POSITIVE_TRAIN_SITE;QD=16.95;ReadPosRankSum=2.202;SOR=0.859;VQSLOD=4.91;culprit=FS GT:AD:DP:GQ:PL 0/1:11,13:24:99:435,0,357 -chr6 46841306 rs220675 T C 195.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.97;SOR=0.941;VQSLOD=5.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,7:7:21:224,21,0 -chr6 46846277 rs220668 G A 565.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.42;SOR=5.549;VQSLOD=6.31;culprit=FS GT:AD:DP:GQ:PL 1/1:0,15:15:45:594,45,0 -chr6 46847501 rs2273265 T G 803.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=5.965;ClippingRankSum=0.700;DB;DP=55;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.735;POSITIVE_TRAIN_SITE;QD=14.61;ReadPosRankSum=1.889;SOR=1.223;VQSLOD=5.17;culprit=FS GT:AD:DP:GQ:PL 0/1:31,23:54:99:832,0,1017 -chr6 46849057 rs11760108 G T 191.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.980;ClippingRankSum=0.068;DB;DP=15;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=0.299;POSITIVE_TRAIN_SITE;QD=12.78;ReadPosRankSum=0.201;SOR=0.693;VQSLOD=6.72;culprit=FS GT:AD:DP:GQ:PL 0/1:7,7:14:99:220,0,248 -chr6 46852193 rs220663 C T 254.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.99;SOR=4.174;VQSLOD=7.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,7:7:21:283,21,0 -chr6 46855734 . C CAGGGAAGAGGACCCAGTAGTTTATCTGCCCA 53.70 PASS AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=5.93;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 46856100 rs678312 G A 5756.77 PASS AC=2;AF=1.00;AN=2;DB;DP=152;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.73;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.10;SOR=1.091;VQSLOD=6.42;culprit=FS GT:AD:DP:GQ:PL 1/1:0,152:152:99:5785,457,0 -chr6 46858081 rs9472896 T C 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=2.303;VQSLOD=7.76;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 46867717 rs220702 C T 2958.77 PASS AC=2;AF=1.00;AN=2;DB;DP=78;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.40;SOR=3.316;VQSLOD=6.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,78:78:99:2987,235,0 -chr6 46867898 rs3215601 TA T 1316.73 PASS AC=2;AF=1.00;AN=2;DB;DP=41;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.26;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.12;SOR=5.892;VQSLOD=4.96;culprit=FS GT:AD:DP:GQ:PL 1/1:0,38:38:99:1354,114,0 -chr6 46869895 rs220698 T G 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.36;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 46874325 rs114267112 T G 1871.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=5.381;ClippingRankSum=1.525;DB;DP=109;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.943;POSITIVE_TRAIN_SITE;QD=17.17;ReadPosRankSum=2.083;SOR=0.752;VQSLOD=2.72;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:53,56:109:99:1900,0,1690 -chr6 46895158 rs6458530 C T 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.44;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 46928378 rs2396803 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46929606 rs1889578 T C 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.59;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 46931019 rs4714972 T G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46932290 rs9472940 T C 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:32:40,0,32 -chr6 46935422 rs9296519 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 46980115 rs1226479 G A 103.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.036;ClippingRankSum=0.365;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.133;POSITIVE_TRAIN_SITE;QD=10.38;ReadPosRankSum=0.741;SOR=0.412;VQSLOD=6.30;culprit=FS GT:AD:DP:GQ:PL 0/1:6,4:10:99:132,0,220 -chr6 46986916 rs1226496 G A 100.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.01;SOR=1.609;VQSLOD=8.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:128,12,0 -chr6 47015046 rs1352665 G T 49.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=9.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 47029819 rs945217 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47037438 rs1226539 G A 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.26;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 47079304 rs10948329 T G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47106677 . T C 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47116726 rs2003031 C T 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=26.37;SOR=2.303;VQSLOD=6.47;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 47163022 rs76480727 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47176242 rs11368956 C CA 44.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=0.693;VQSLOD=8.41;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 47200360 . AAC A 225.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.751;ClippingRankSum=0.751;DP=18;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-0.751;QD=12.54;ReadPosRankSum=-0.751;SOR=3.056;VQSLOD=4.97;culprit=FS GT:AD:DP:GQ:PL 0/1:1,11:12:4:212,0,4 -chr6 47200703 rs202137000 A C 155.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-6.080;ClippingRankSum=0.291;DB;DP=89;FS=88.069;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=0;MQRankSum=-0.508;QD=1.75;ReadPosRankSum=-1.601;SOR=6.868;VQSLOD=-1.420e+01;culprit=FS GT:AD:DP:GQ:PL 0/1:59,30:89:99:184,0,1744 -chr6 47228836 rs4715001 C A 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=8.80;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 47228912 rs10807350 G A 61.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.68;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 -chr6 47369341 rs4301296 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47373447 rs1931826 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47425273 rs1889494 T C 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.52;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 47450481 rs9395261 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47462615 rs2184398 T C 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.42;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 47464881 rs62410680 G A 107.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;QD=23.04;SOR=2.833;VQSLOD=7.19;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 47464883 rs202187543 G GT 98.25 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;QD=32.75;SOR=2.833;VQSLOD=6.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 47467043 rs34508069 A ATG 34.71 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.44;MQ0=0;POSITIVE_TRAIN_SITE;QD=11.57;SOR=0.693;VQSLOD=7.53;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 -chr6 47470146 rs1564926 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47489866 rs62410686 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47494842 rs35617629 T TC 24.72 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.44;MQ0=0;QD=8.24;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 -chr6 47512229 rs6915993 C T 472.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.902;ClippingRankSum=-1.520;DB;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.645;POSITIVE_TRAIN_SITE;QD=16.88;ReadPosRankSum=-0.369;SOR=0.836;VQSLOD=5.04;culprit=FS GT:AD:DP:GQ:PL 0/1:13,15:28:99:501,0,447 -chr6 47512590 rs6916578 C T 344.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.172;ClippingRankSum=-0.793;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.340;POSITIVE_TRAIN_SITE;QD=21.55;ReadPosRankSum=-0.566;SOR=1.609;VQSLOD=6.22;culprit=FS GT:AD:DP:GQ:PL 0/1:5,11:16:99:373,0,169 -chr6 47522357 rs9473132 G A 2114.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.279;ClippingRankSum=0.098;DB;DP=140;FS=1.431;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.117;POSITIVE_TRAIN_SITE;QD=15.11;ReadPosRankSum=-0.616;SOR=0.874;VQSLOD=2.05;culprit=DP GT:AD:DP:GQ:PL 0/1:66,74:140:99:2143,0,2115 -chr6 47530422 rs9395277 A C 559.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.99;SOR=5.549;VQSLOD=6.68;culprit=QD GT:AD:DP:GQ:PL 1/1:0,15:15:45:588,45,0 -chr6 47532683 rs9395278 T A 63.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=9.00;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 47545058 rs978448 C T 76.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;ClippingRankSum=0.406;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.988;POSITIVE_TRAIN_SITE;QD=12.79;ReadPosRankSum=0.406;SOR=2.093;VQSLOD=6.60;culprit=FS GT:AD:DP:GQ:PL 0/1:3,3:6:99:105,0,105 -chr6 47548672 rs1014001 C A 2124.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.361;ClippingRankSum=1.150;DB;DP=186;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=1.434;POSITIVE_TRAIN_SITE;QD=11.42;ReadPosRankSum=-1.001;SOR=0.701;VQSLOD=1.41;culprit=FS GT:AD:DP:GQ:PL 0/1:112,73:185:99:2153,0,3635 -chr6 47549586 rs6926592 A T 31.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.47;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=3.53;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=5.09;culprit=QD GT:AD:DP:GQ:PL 0/1:2,2:4:60:60,0,65 -chr6 47549883 rs2275446 T C 1040.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=5.815;ClippingRankSum=-1.023;DB;DP=59;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.902;POSITIVE_TRAIN_SITE;QD=17.64;ReadPosRankSum=1.327;SOR=1.609;VQSLOD=5.52;culprit=FS GT:AD:DP:GQ:PL 0/1:30,29:59:99:1069,0,967 -chr6 47563692 rs2039503 C T 15612.77 PASS AC=2;AF=1.00;AN=2;DB;DP=434;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=32.86;SOR=1.288;VQSLOD=0.729;culprit=DP GT:AD:DP:GQ:PL 1/1:0,433:433:99:15641,1302,0 -chr6 47577064 rs9395287 G A 1930.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.080;ClippingRankSum=-0.414;DB;DP=155;FS=5.202;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=1.011;POSITIVE_TRAIN_SITE;QD=12.46;ReadPosRankSum=1.551;SOR=0.345;VQSLOD=2.02;culprit=DP GT:AD:DP:GQ:PL 0/1:89,66:155:99:1959,0,2911 -chr6 47591856 rs10948368 T C 837.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.469;ClippingRankSum=1.334;DB;DP=42;FS=3.025;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.826;POSITIVE_TRAIN_SITE;QD=19.95;ReadPosRankSum=1.309;SOR=0.151;VQSLOD=2.32;culprit=QD GT:AD:DP:GQ:PL 0/1:18,24:42:99:866,0,595 -chr6 47592328 rs11309569 GT G 75.25 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.08;SOR=1.179;VQSLOD=8.27;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:112,9,0 -chr6 47611404 rs13196954 C G 36.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.937;ClippingRankSum=0.000;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=5.25;ReadPosRankSum=0.937;SOR=0.446;VQSLOD=4.88;culprit=QD GT:AD:DP:GQ:PL 0/1:4,3:7:65:65,0,111 -chr6 47611442 rs7766527 T C 84.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=-0.421;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.017;POSITIVE_TRAIN_SITE;QD=10.60;ReadPosRankSum=0.421;SOR=1.609;VQSLOD=4.55;culprit=FS GT:AD:DP:GQ:PL 0/1:4,4:8:99:113,0,102 -chr6 47624115 rs1485782 C T 140.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;ClippingRankSum=0.198;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.03;MQ0=0;MQRankSum=-0.922;POSITIVE_TRAIN_SITE;QD=20.11;ReadPosRankSum=1.495;SOR=1.609;VQSLOD=5.61;culprit=FS GT:AD:DP:GQ:PL 0/1:2,5:7:57:169,0,57 -chr6 47624129 rs1485783 G A 221.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.733;ClippingRankSum=-0.898;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.65;MQ0=0;MQRankSum=-0.480;POSITIVE_TRAIN_SITE;QD=22.18;ReadPosRankSum=0.480;SOR=2.303;VQSLOD=5.41;culprit=FS GT:AD:DP:GQ:PL 0/1:2,8:10:57:250,0,57 -chr6 47624239 rs1485784 A G 779.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.260;ClippingRankSum=-1.087;DB;DP=42;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=0;MQRankSum=-0.455;POSITIVE_TRAIN_SITE;QD=18.57;ReadPosRankSum=-1.744;SOR=0.286;VQSLOD=5.10;culprit=FS GT:AD:DP:GQ:PL 0/1:19,23:42:99:808,0,614 -chr6 47624299 rs9369730 A G 990.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.981;ClippingRankSum=0.405;DB;DP=68;FS=2.459;MLEAC=1;MLEAF=0.500;MQ=56.52;MQ0=0;MQRankSum=-0.459;POSITIVE_TRAIN_SITE;QD=14.57;ReadPosRankSum=2.549;SOR=0.389;VQSLOD=2.90;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:29,35:64:99:1019,0,894 -chr6 47624633 rs1021231 G A 201.84 PASS AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.04;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.64;SOR=3.912;VQSLOD=7.41;culprit=FS GT:AD:DP:GQ:PL 1/1:0,6:6:18:230,18,0 -chr6 47626149 rs6934553 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47626490 rs10456129 G C 47.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=15.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=6.40;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:30:76,0,30 -chr6 47626685 rs6935668 C T 505.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.678;ClippingRankSum=-0.091;DB;DP=50;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.677;POSITIVE_TRAIN_SITE;QD=10.12;ReadPosRankSum=-0.677;SOR=0.670;VQSLOD=4.29;culprit=FS GT:AD:DP:GQ:PL 0/1:32,18:50:99:534,0,1085 -chr6 47626833 rs12201065 C A 1126.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.697;ClippingRankSum=-0.211;DB;DP=79;FS=1.842;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.624;POSITIVE_TRAIN_SITE;QD=14.26;ReadPosRankSum=2.098;SOR=0.509;VQSLOD=3.19;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:42,37:79:99:1155,0,1430 -chr6 47631622 rs2396829 G T 13.72 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=6.86;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 -chr6 47641307 rs1411049 G C 1221.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-6.168;ClippingRankSum=0.230;DB;DP=74;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.479;POSITIVE_TRAIN_SITE;QD=16.51;ReadPosRankSum=-0.340;SOR=1.061;VQSLOD=4.74;culprit=FS GT:AD:DP:GQ:PL 0/1:31,43:74:99:1250,0,1019 -chr6 47645772 rs9369734 G T 131.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.387;ClippingRankSum=-0.717;DB;DP=11;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=1.186;POSITIVE_TRAIN_SITE;QD=11.98;ReadPosRankSum=1.031;SOR=0.551;VQSLOD=4.95;culprit=FS GT:AD:DP:GQ:PL 0/1:6,5:11:99:160,0,198 -chr6 47646468 rs6929227 T C 36.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=12.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=5.87;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:33:65,0,33 -chr6 47646842 rs6907125 A G 1474.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.856;ClippingRankSum=0.375;DB;DP=112;FS=1.527;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-0.670;POSITIVE_TRAIN_SITE;QD=13.17;ReadPosRankSum=-0.351;SOR=0.896;VQSLOD=2.99;culprit=DP GT:AD:DP:GQ:PL 0/1:57,54:111:99:1503,0,1770 -chr6 47647004 rs6911739 C T 236.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.835;ClippingRankSum=-0.289;DB;DP=14;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.536;POSITIVE_TRAIN_SITE;QD=16.91;ReadPosRankSum=0.289;SOR=0.495;VQSLOD=6.19;culprit=FS GT:AD:DP:GQ:PL 0/1:4,8:12:99:265,0,101 -chr6 47647593 rs58870329 GA G 32.74 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=10.91;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=6.02;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:30:70,0,30 -chr6 47649222 rs8180544 T G 3766.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.617;ClippingRankSum=-0.635;DB;DP=262;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=-0.348;POSITIVE_TRAIN_SITE;QD=14.38;ReadPosRankSum=1.474;SOR=0.706;VQSLOD=1.98;culprit=FS GT:AD:DP:GQ:PL 0/1:130,131:261:99:3795,0,4054 -chr6 47649265 rs17541107 T A 4039.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.520;ClippingRankSum=0.331;DB;DP=283;FS=5.506;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.377;POSITIVE_TRAIN_SITE;QD=14.27;ReadPosRankSum=1.570;SOR=0.994;VQSLOD=1.83;culprit=DP GT:AD:DP:GQ:PL 0/1:148,135:283:99:4068,0,4356 -chr6 47649573 rs10807371 C T 3884.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.363;ClippingRankSum=0.166;DB;DP=210;FS=0.513;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=18.50;ReadPosRankSum=2.787;SOR=0.633;VQSLOD=1.64;culprit=FS GT:AD:DP:GQ:PL 0/1:110,99:209:99:3913,0,7372 -chr6 47649574 rs10807372 A G 3884.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=5.254;ClippingRankSum=0.771;DB;DP=211;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=1.085;POSITIVE_TRAIN_SITE;QD=18.41;ReadPosRankSum=2.423;SOR=0.713;VQSLOD=1.59;culprit=FS GT:AD:DP:GQ:PL 0/1:108,102:210:99:3913,0,7372 -chr6 47649694 rs9381594 A G 2384.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.217;ClippingRankSum=0.797;DB;DP=160;FS=5.307;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.869;POSITIVE_TRAIN_SITE;QD=14.90;ReadPosRankSum=0.046;SOR=1.179;VQSLOD=2.22;culprit=DP GT:AD:DP:GQ:PL 0/1:82,78:160:99:2413,0,2636 -chr6 47653485 rs9369736 A G 580.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.376;ClippingRankSum=-0.637;DB;DP=39;FS=6.870;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.099;POSITIVE_TRAIN_SITE;QD=14.89;ReadPosRankSum=1.119;SOR=2.200;VQSLOD=2.66;culprit=FS GT:AD:DP:GQ:PL 0/1:22,17:39:99:609,0,665 -chr6 47653536 rs9381596 A G 676.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.398;ClippingRankSum=-1.699;DB;DP=50;FS=5.655;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.621;POSITIVE_TRAIN_SITE;QD=13.54;ReadPosRankSum=1.097;SOR=1.197;VQSLOD=1.88;culprit=FS GT:AD:DP:GQ:PL 0/1:26,24:50:99:705,0,787 -chr6 47654591 rs10948376 G T 642.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.972;ClippingRankSum=-0.822;DB;DP=39;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.782;POSITIVE_TRAIN_SITE;QD=16.48;ReadPosRankSum=-0.752;SOR=1.085;VQSLOD=3.73;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:14,20:34:99:671,0,497 -chr6 47654662 rs10485315 A G 2893.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=7.315;ClippingRankSum=0.398;DB;DP=167;FS=1.004;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.357;POSITIVE_TRAIN_SITE;QD=17.33;ReadPosRankSum=2.188;SOR=0.957;VQSLOD=2.61;culprit=FS GT:AD:DP:GQ:PL 0/1:84,83:167:99:2922,0,2748 -chr6 47654742 rs9296573 A T 4359.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.866;ClippingRankSum=0.983;DB;DP=296;FS=5.331;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=0.493;POSITIVE_TRAIN_SITE;QD=14.73;ReadPosRankSum=-1.261;SOR=0.468;VQSLOD=1.31;culprit=DP GT:AD:DP:GQ:PL 0/1:143,153:296:99:4388,0,4431 -chr6 47654817 rs1556133 C A 3193.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-6.266;ClippingRankSum=-0.767;DB;DP=141;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.607;POSITIVE_TRAIN_SITE;QD=22.65;ReadPosRankSum=0.439;SOR=0.716;VQSLOD=2.57;culprit=FS GT:AD:DP:GQ:PL 0/1:57,84:141:99:3222,0,2060 -chr6 47654831 rs1556132 A G 3144.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=5.124;ClippingRankSum=-0.737;DB;DP=121;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.550;POSITIVE_TRAIN_SITE;QD=25.99;ReadPosRankSum=0.045;SOR=0.730;VQSLOD=2.91;culprit=FS GT:AD:DP:GQ:PL 0/1:47,74:121:99:3173,0,1780 -chr6 47654864 rs1556131 T G 1356.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.916;ClippingRankSum=1.761;DB;DP=69;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.023;POSITIVE_TRAIN_SITE;QD=19.66;ReadPosRankSum=-0.030;SOR=0.980;VQSLOD=4.41;culprit=FS GT:AD:DP:GQ:PL 0/1:30,39:69:99:1385,0,976 -chr6 47661115 rs6901702 T C 90.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.09;SOR=2.833;VQSLOD=7.91;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:118,9,0 -chr6 47661248 rs36010404 AG A 335.73 PASS AC=2;AF=1.00;AN=2;DB;DP=12;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.98;SOR=4.977;VQSLOD=6.17;culprit=FS GT:AD:DP:GQ:PL 1/1:0,11:11:33:373,33,0 -chr6 47661260 rs200900695 AC A 126.76 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.589;ClippingRankSum=-0.354;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.65;MQ0=0;MQRankSum=-1.768;POSITIVE_TRAIN_SITE;QD=7.92;ReadPosRankSum=1.061;SOR=2.494;VQSLOD=4.52;culprit=FS GT:AD:DP:GQ:PL 0/1:2,9:11:22:164,0,22 -chr6 47661387 rs9395311 A G 2320.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.015;ClippingRankSum=-0.577;DB;DP=139;FS=8.901;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-0.615;POSITIVE_TRAIN_SITE;QD=16.70;ReadPosRankSum=2.635;SOR=0.237;VQSLOD=1.11;culprit=FS GT:AD:DP:GQ:PL 0/1:64,75:139:99:2349,0,1921 -chr6 47675922 rs16876334 C T 1527.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.988;ClippingRankSum=-0.373;DB;DP=82;FS=4.427;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.181;POSITIVE_TRAIN_SITE;QD=18.63;ReadPosRankSum=0.624;SOR=1.413;VQSLOD=1.23;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:37,45:82:99:1556,0,1063 -chr6 47676150 rs9369737 C T 269.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.291;ClippingRankSum=1.732;DB;DP=23;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.283;POSITIVE_TRAIN_SITE;QD=11.73;ReadPosRankSum=-0.346;SOR=0.368;VQSLOD=5.18;culprit=FS GT:AD:DP:GQ:PL 0/1:14,9:23:99:298,0,504 -chr6 47678455 rs11356177 CT C 1687.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.012;ClippingRankSum=-0.222;DB;DP=162;FS=0.656;MLEAC=1;MLEAF=0.500;MQ=60.33;MQ0=0;MQRankSum=1.477;POSITIVE_TRAIN_SITE;QD=10.42;ReadPosRankSum=0.632;SOR=0.809;VQSLOD=1.77;culprit=FS GT:AD:DP:GQ:PL 0/1:80,76:156:99:1725,0,2007 -chr6 47678678 rs944056 C G 3493.77 PASS AC=2;AF=1.00;AN=2;DB;DP=91;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.59;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.34;SOR=2.758;VQSLOD=7.40;culprit=FS GT:AD:DP:GQ:PL 1/1:0,90:90:99:3522,271,0 -chr6 47678718 rs1318391 C G 857.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.618;ClippingRankSum=0.693;DB;DP=61;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.080;POSITIVE_TRAIN_SITE;QD=14.06;ReadPosRankSum=0.970;SOR=0.439;VQSLOD=5.75;culprit=FS GT:AD:DP:GQ:PL 0/1:35,26:61:99:886,0,1329 -chr6 47678848 rs199503700 CAA C 43.74 PASS AC=1;AF=0.500;AN=2;DB;DP=2;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.87;SOR=2.303;VQSLOD=8.58;culprit=FS GT:AD:DP:GQ:PL 0/1:0,2:2:25:81,0,25 -chr6 47678861 rs9381602 A G 52.78 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.93;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:25:81,0,25 -chr6 47680450 rs871654 A C 516.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.618;ClippingRankSum=-0.634;DB;DP=21;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.410;POSITIVE_TRAIN_SITE;QD=24.61;ReadPosRankSum=0.634;SOR=1.508;VQSLOD=5.59;culprit=FS GT:AD:DP:GQ:PL 0/1:7,14:21:99:545,0,211 -chr6 47681494 rs6916562 T C 3414.77 PASS AC=2;AF=1.00;AN=2;DB;DP=86;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.92;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.90;SOR=5.235;VQSLOD=6.11;culprit=FS GT:AD:DP:GQ:PL 1/1:0,86:86:99:3443,259,0 -chr6 47682604 rs9369738 A C 6287.77 PASS AC=2;AF=1.00;AN=2;DB;DP=181;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.74;SOR=1.468;VQSLOD=6.07;culprit=QD GT:AD:DP:GQ:PL 1/1:0,179:179:99:6316,538,0 -chr6 47682949 rs16876369 C T 1708.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.057;ClippingRankSum=-0.481;DB;DP=110;FS=7.189;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.072;POSITIVE_TRAIN_SITE;QD=15.53;ReadPosRankSum=0.146;SOR=1.458;VQSLOD=1.58;culprit=FS GT:AD:DP:GQ:PL 0/1:54,56:110:99:1737,0,1465 -chr6 47683057 rs41452951 A G 376.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.298;ClippingRankSum=-0.209;DB;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=0.070;POSITIVE_TRAIN_SITE;QD=13.46;ReadPosRankSum=0.070;SOR=0.460;VQSLOD=5.39;culprit=FS GT:AD:DP:GQ:PL 0/1:16,12:28:99:405,0,546 -chr6 47684591 rs1360157 G A 2096.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.035;ClippingRankSum=0.291;DB;DP=146;FS=1.305;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.615;POSITIVE_TRAIN_SITE;QD=14.36;ReadPosRankSum=0.971;SOR=0.572;VQSLOD=3.15;culprit=DP GT:AD:DP:GQ:PL 0/1:74,71:145:99:2125,0,2159 -chr6 47686101 rs6914013 T C 9061.77 PASS AC=2;AF=1.00;AN=2;DB;DP=255;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.19;SOR=1.281;VQSLOD=5.11;culprit=FS GT:AD:DP:GQ:PL 1/1:0,254:254:99:9090,763,0 -chr6 47686235 rs11754756 C A 1895.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.892;ClippingRankSum=1.540;DB;DP=110;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=0.867;POSITIVE_TRAIN_SITE;QD=17.23;ReadPosRankSum=-0.771;SOR=0.905;VQSLOD=3.88;culprit=FS GT:AD:DP:GQ:PL 0/1:50,60:110:99:1924,0,1695 -chr6 47686397 rs11476874 AT A 63.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=-0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=62.13;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=12.75;ReadPosRankSum=0.358;SOR=1.022;VQSLOD=6.60;culprit=FS GT:AD:DP:GQ:PL 0/1:2,3:5:66:101,0,66 -chr6 47690579 rs1329522 T C 91.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.76;SOR=0.693;VQSLOD=6.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:119,12,0 -chr6 47690601 rs35597357 T C 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.026;QD=7.44;ReadPosRankSum=0.000;SOR=0.693 GT:AD:DP:GQ:PL 0/1:2,2:4:37:58,0,37 -chr6 47690613 rs1329523 G A 81.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.09;SOR=1.179;VQSLOD=8.50;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:109,9,0 -chr6 47696780 rs2282337 C T 36.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.380;ClippingRankSum=-0.720;DB;DP=6;FS=3.310;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=6.13;ReadPosRankSum=-0.720;SOR=2.303;VQSLOD=2.06;culprit=QD GT:AD:DP:GQ:PL 0/1:4,2:6:65:65,0,81 -chr6 47698280 rs1329540 G A 94.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=1.179;VQSLOD=8.91;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:122,9,0 -chr6 47698303 rs1329539 C T 94.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=1.179;VQSLOD=7.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:122,9,0 -chr6 47703969 rs949680 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47707247 rs72864549 C T 37.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.87;SOR=2.303;VQSLOD=6.90;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:65,6,0 -chr6 47708230 rs12199415 A G 96.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.09;SOR=1.179;VQSLOD=7.86;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:124,9,0 -chr6 47708267 rs9473166 C T 93.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.09;SOR=1.179;VQSLOD=6.97;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:121,9,0 -chr6 47712313 rs9349429 T G 41.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.87;SOR=2.303;VQSLOD=8.76;culprit=QD GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 -chr6 47714073 rs9367302 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47720533 rs61744507 G A 144.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.876;ClippingRankSum=-1.652;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.361;POSITIVE_TRAIN_SITE;QD=16.09;ReadPosRankSum=1.881;SOR=0.892;VQSLOD=5.73;culprit=FS GT:AD:DP:GQ:PL 0/1:4,5:9:99:173,0,134 -chr6 47720824 rs2039141 A G 2982.77 PASS AC=2;AF=1.00;AN=2;DB;DP=82;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.72;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.60;SOR=1.697;VQSLOD=5.16;culprit=FS GT:AD:DP:GQ:PL 1/1:0,82:82:99:3011,247,0 -chr6 47740398 rs1329529 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47746444 rs10485318 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47749539 rs9395320 A G 59.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=9.35;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 47749728 rs7741473 T G 1371.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.498;ClippingRankSum=1.007;DB;DP=64;FS=3.910;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=0.168;POSITIVE_TRAIN_SITE;QD=21.43;ReadPosRankSum=-0.210;SOR=0.253;VQSLOD=2.29;culprit=QD GT:AD:DP:GQ:PL 0/1:23,41:64:99:1400,0,654 -chr6 47754498 rs1329543 A G 352.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.647;ClippingRankSum=-0.208;DB;DP=26;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.052;POSITIVE_TRAIN_SITE;QD=13.57;ReadPosRankSum=0.052;SOR=0.446;VQSLOD=5.83;culprit=FS GT:AD:DP:GQ:PL 0/1:15,11:26:99:381,0,529 -chr6 47754538 rs6900985 T C 166.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.859;ClippingRankSum=-1.156;DB;DP=17;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.653;POSITIVE_TRAIN_SITE;QD=9.81;ReadPosRankSum=0.653;SOR=0.293;VQSLOD=5.20;culprit=FS GT:AD:DP:GQ:PL 0/1:11,6:17:99:195,0,378 -chr6 47763514 rs139235050 TCACACA T 98.25 PASS AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.10;MQ0=0;QD=19.65;SOR=2.833;VQSLOD=6.81;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 47808012 rs474725 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47822105 rs532671 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47826378 rs476873 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47841953 rs4715047 G T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47845813 rs1887899 G T 171.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.38;SOR=3.611;VQSLOD=7.20;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:200,15,0 -chr6 47847179 rs3799276 A G 11221.77 PASS AC=2;AF=1.00;AN=2;DB;DP=302;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.72;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.02;SOR=1.221;VQSLOD=2.80;culprit=FS GT:AD:DP:GQ:PL 1/1:0,301:301:99:11250,905,0 -chr6 47847401 rs2068006 A G 6414.77 PASS AC=2;AF=1.00;AN=2;DB;DP=184;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.86;SOR=0.832;VQSLOD=4.02;culprit=QD GT:AD:DP:GQ:PL 1/1:0,182:182:99:6443,547,0 -chr6 47847683 rs9367307 A T 3379.77 PASS AC=2;AF=1.00;AN=2;DB;DP=142;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.80;SOR=3.095;VQSLOD=3.37;culprit=FS GT:AD:DP:GQ:PL 1/1:0,121:121:99:3408,364,0 -chr6 47862643 rs113155505 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47865882 rs4715053 G C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47869426 rs1360080 A G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=9.52;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 47869448 rs1360081 G A 125.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.26;SOR=1.609;VQSLOD=7.95;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:153,12,0 -chr6 47871871 rs13194591 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.67;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 47871877 . A G 62.74 PASS AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.51;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 47927739 . A T 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47941339 rs2753188 G A 61.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=6.28;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 -chr6 47954722 rs2145363 C A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 47977018 rs2753194 C A 684.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.070;ClippingRankSum=1.380;DB;DP=36;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.995;POSITIVE_TRAIN_SITE;QD=19.02;ReadPosRankSum=1.508;SOR=1.061;VQSLOD=4.96;culprit=FS GT:AD:DP:GQ:PL 0/1:15,21:36:99:713,0,543 -chr6 47977136 rs45599036 C T 79.78 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;POSITIVE_TRAIN_SITE;QD=19.94;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=5.45;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:26:108,0,26 -chr6 48005879 rs12205869 G A 45.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=0.693;VQSLOD=9.01;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 -chr6 48009812 . A C 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 -chr6 48015295 rs618543 T G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48015693 rs332554 A G 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=7.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 48026377 rs647942 A G 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=9.17;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 48032884 rs75735764 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48036051 rs201541883 A C 779.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-6.322;ClippingRankSum=-0.178;DB;DP=120;FS=165.662;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-0.683;QD=6.50;ReadPosRankSum=-4.265;SOR=8.379;VQSLOD=-6.204e+01;culprit=FS GT:AD:DP:GQ:PL 0/1:52,65:117:99:808,0,1315 -chr6 48083008 rs6908563 G A 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.84;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 48117685 rs12523977 C G 501.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.424;ClippingRankSum=0.073;DB;DP=38;FS=1.785;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.833;POSITIVE_TRAIN_SITE;QD=13.20;ReadPosRankSum=-2.675;SOR=1.329;VQSLOD=1.85;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:20,18:38:99:530,0,640 -chr6 48131753 rs1331118 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48172099 . G GGGA 46.70 PASS AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=23.35;SOR=0.693;VQSLOD=5.94;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 48195386 . A G 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48214766 rs2456916 A G 38.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=12.92;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=5.88;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:33:67,0,33 -chr6 48214812 rs2503669 C G 78.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.754;ClippingRankSum=0.937;DB;DP=7;FS=15.441;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.550;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=11.25;ReadPosRankSum=1.300;SOR=2.775;VQSLOD=0.030;culprit=FS GT:AD:DP:GQ:PL 0/1:4,3:7:99:107,0,141 -chr6 48214977 rs2503670 A G 44.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.000;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=11.19;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=6.40;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:71:73,0,71 -chr6 48215008 rs2496375 G A 41.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=10.44;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=6.07;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:70:70,0,71 -chr6 48225108 . A G 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48262773 rs13202212 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48282517 rs11758955 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48282542 rs545090 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48396334 rs9473361 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48445933 rs1121646 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48448275 rs9473387 A T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48449928 . C A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48450548 rs9784854 G A 47.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=2.303;VQSLOD=7.59;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 48456067 rs148792649 CAGTCTTGAAGACAAAATGCTAACATGTAATAAGAAAATATTTGA C 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=7.01;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 48456290 rs7754822 G T 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 48456315 rs9473391 A T 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=9.25;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 48464593 rs9473403 G T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48467616 rs12206390 A G 65.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.76;SOR=1.179;VQSLOD=8.09;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:93,9,0 -chr6 48468120 rs6915049 A T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48592097 . G A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48596846 rs2912621 T G 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 48609036 rs963049 G C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48615474 rs2433657 A T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48750072 rs2495881 T C 75.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.09;SOR=2.833;VQSLOD=7.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:103,9,0 -chr6 48792612 rs2495863 C T 62.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.73;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 48811854 . C A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48825657 rs1938202 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48899692 rs10948458 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 48919773 rs16878430 G A 235.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.540;ClippingRankSum=-0.212;DB;DP=16;FS=4.467;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.318;POSITIVE_TRAIN_SITE;QD=14.74;ReadPosRankSum=-1.059;SOR=0.525;VQSLOD=3.12;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:7,9:16:99:264,0,243 -chr6 48920376 rs12204534 C T 96.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.09;SOR=2.833;VQSLOD=7.58;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:124,9,0 -chr6 49011686 rs35984632 A AT 50.25 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=63.51;MQ0=0;QD=16.75;SOR=1.179;VQSLOD=7.07;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:87,9,0 -chr6 49022228 rs6458657 C A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49036510 rs12194577 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49045630 rs9367346 A T 789.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.471;ClippingRankSum=-1.379;DB;DP=53;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.098;POSITIVE_TRAIN_SITE;QD=14.90;ReadPosRankSum=2.233;SOR=0.793;VQSLOD=5.52;culprit=FS GT:AD:DP:GQ:PL 0/1:27,26:53:99:818,0,792 -chr6 49052341 rs6458676 A G 38.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=7.75;ReadPosRankSum=-0.358;SOR=1.179;VQSLOD=5.43;culprit=QD GT:AD:DP:GQ:PL 0/1:2,3:5:34:67,0,34 -chr6 49083404 . A G 43.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.000;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.026;QD=10.94;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=3.54;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:61:72,0,61 -chr6 49169185 rs113197207 C CTTCT 77.25 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.53;SOR=0.693;VQSLOD=8.18;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:9:114,9,0 -chr6 49199384 rs570913 T G 15.65 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=15.65;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0 -chr6 49209747 rs9463466 G T 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.39;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 49212193 rs492254 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49218084 rs7756663 G A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 49218093 rs11453208 A AT 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=6.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 49397107 . A G 12.06 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:26:40,0,26 -chr6 49414272 . A G 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49415351 . TA T 91.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.540;ClippingRankSum=-0.501;DP=115;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.85;MQ0=0;MQRankSum=0.642;POSITIVE_TRAIN_SITE;QD=0.80;ReadPosRankSum=0.146;SOR=0.653;VQSLOD=3.81;culprit=FS GT:AD:DP:GQ:PL 0/1:57,17:74:99:129,0,1146 -chr6 49437853 rs11333073 AT A 27.74 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.412;ClippingRankSum=-0.483;DB;DP=50;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=0;MQRankSum=0.985;QD=0.55;ReadPosRankSum=0.770;SOR=0.976 GT:AD:DP:GQ:PL 0/1:38,8:46:65:65,0,808 -chr6 49456545 rs2501965 G A 816.77 PASS AC=2;AF=1.00;AN=2;DB;DP=22;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.39;SOR=6.273;VQSLOD=4.58;culprit=FS GT:AD:DP:GQ:PL 1/1:0,22:22:66:845,66,0 -chr6 49459978 rs2501968 A G 4668.77 PASS AC=2;AF=1.00;AN=2;DB;DP=126;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.08;SOR=1.981;VQSLOD=6.45;culprit=FS GT:AD:DP:GQ:PL 1/1:0,124:124:99:4697,373,0 -chr6 49460152 rs1471539 A G 177.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.65;SOR=3.611;VQSLOD=5.84;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:206,15,0 -chr6 49479750 rs13193063 T C 340.77 PASS AC=2;AF=1.00;AN=2;DB;DP=12;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.40;SOR=1.445;VQSLOD=6.20;culprit=FS GT:AD:DP:GQ:PL 1/1:0,12:12:36:369,36,0 -chr6 49479775 rs1480615 A T 224.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.11;SOR=2.584;VQSLOD=7.65;culprit=FS GT:AD:DP:GQ:PL 1/1:0,7:7:21:253,21,0 -chr6 49480339 rs9463493 A G 64.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=1.179;VQSLOD=8.26;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:92,9,0 -chr6 49494241 rs9367359 A G 3361.77 PASS AC=2;AF=1.00;AN=2;DB;DP=95;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.60;SOR=0.826;VQSLOD=7.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,94:94:99:3390,283,0 -chr6 49495862 rs6458696 T G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49497461 rs2396905 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49508103 rs9463500 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49515525 rs4715136 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49518914 rs6919674 C G 44.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.37;SOR=2.303;VQSLOD=8.57;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:72,6,0 -chr6 49522920 . T A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49528183 rs6899583 A G 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=7.73;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 49537956 rs36081197 T A 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.79;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 49559793 rs10948514 G T 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=8.84;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 49596219 rs4711931 T C 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.20;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 49646966 rs7763840 T C 66.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.09;SOR=1.179;VQSLOD=8.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:94,9,0 -chr6 49650193 rs148454607 CCCT C 84.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=-0.727;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=62.13;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=16.95;ReadPosRankSum=0.727;SOR=0.916;VQSLOD=6.11;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:37:122,0,37 -chr6 49660418 rs12624 A C 1647.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.101;ClippingRankSum=-1.338;DB;DP=95;FS=5.883;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=-1.323;POSITIVE_TRAIN_SITE;QD=17.34;ReadPosRankSum=0.011;SOR=1.333;VQSLOD=1.55;culprit=FS GT:AD:DP:GQ:PL 0/1:42,53:95:99:1676,0,1201 -chr6 49663465 rs2248263 G A 603.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.236;ClippingRankSum=0.133;DB;DP=33;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.399;POSITIVE_TRAIN_SITE;QD=18.30;ReadPosRankSum=0.589;SOR=0.957;VQSLOD=5.69;culprit=FS GT:AD:DP:GQ:PL 0/1:14,18:32:99:632,0,410 -chr6 49665120 rs10548881 GGT G 34.71 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=63.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=11.57;SOR=2.303;VQSLOD=8.54;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 -chr6 49666381 rs515257 G A 145.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.886;ClippingRankSum=-1.798;DB;DP=19;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.395;POSITIVE_TRAIN_SITE;QD=7.67;ReadPosRankSum=1.184;SOR=0.223;VQSLOD=5.06;culprit=QD GT:AD:DP:GQ:PL 0/1:13,6:19:99:174,0,478 -chr6 49668405 rs57295760 T G 1149.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-6.101;ClippingRankSum=0.570;DB;DP=174;FS=322.757;MLEAC=1;MLEAF=0.500;MQ=47.79;MQ0=0;MQRankSum=-5.344;QD=6.61;ReadPosRankSum=-6.450;SOR=9.149;VQSLOD=-2.485e+02;culprit=FS GT:AD:DP:GQ:PL 0/1:77,96:173:99:1178,0,1978 -chr6 49676536 rs699954 C T 48.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=8.45;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 49693598 rs1068276 G A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.41;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 49693612 rs35883674 CT C 93.25 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.08;SOR=1.179;VQSLOD=8.80;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:130,9,0 -chr6 49695232 rs510770 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49701439 rs1864312 C A 1555.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.745;ClippingRankSum=0.346;DB;DP=113;FS=1.849;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.795;POSITIVE_TRAIN_SITE;QD=13.77;ReadPosRankSum=1.613;SOR=0.978;VQSLOD=2.84;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:63,49:112:99:1584,0,2066 -chr6 49701523 rs495335 A G 1861.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.084;ClippingRankSum=-0.565;DB;DP=149;FS=0.622;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.400;POSITIVE_TRAIN_SITE;QD=12.50;ReadPosRankSum=3.925;SOR=0.775;VQSLOD=2.06;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:84,65:149:99:1890,0,2674 -chr6 49703027 rs3823210 G T 73.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.231;ClippingRankSum=-0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=14.75;ReadPosRankSum=-1.231;SOR=1.022;VQSLOD=6.26;culprit=FS GT:AD:DP:GQ:PL 0/1:2,3:5:72:102,0,72 -chr6 49787315 rs5876131 G GT 25.72 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=12.86;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:62,6,0 -chr6 49798102 . C CAGAG 53.70 PASS AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=4.57;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 49803370 rs1652094 A G 290.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.34;SOR=4.407;VQSLOD=6.61;culprit=FS GT:AD:DP:GQ:PL 1/1:0,8:8:24:319,24,0 -chr6 49807422 rs7753886 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49815873 rs373553362 AT A 85.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.243;ClippingRankSum=-0.384;DB;DP=85;FS=2.397;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=1.200;QD=1.01;ReadPosRankSum=0.512;SOR=1.508;VQSLOD=1.09;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:52,14:66:99:123,0,1132 -chr6 49818670 rs780782 T C 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.96;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 49835335 rs1084051 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 49858594 rs2153575 C T 361.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.037;ClippingRankSum=1.977;DB;DP=21;FS=4.722;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.037;POSITIVE_TRAIN_SITE;QD=17.23;ReadPosRankSum=-0.336;SOR=0.127;VQSLOD=3.26;culprit=FS GT:AD:DP:GQ:PL 0/1:7,14:21:99:390,0,186 -chr6 49913981 rs7760672 C T 1758.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.016;ClippingRankSum=0.747;DB;DP=119;FS=1.762;MLEAC=1;MLEAF=0.500;MQ=59.81;MQ0=0;MQRankSum=0.359;POSITIVE_TRAIN_SITE;QD=14.78;ReadPosRankSum=-0.178;SOR=0.963;VQSLOD=3.22;culprit=DP GT:AD:DP:GQ:PL 0/1:58,61:119:99:1787,0,1869 -chr6 49917264 rs9369926 A C 219.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.074;ClippingRankSum=-1.220;DB;DP=17;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.732;POSITIVE_TRAIN_SITE;QD=12.93;ReadPosRankSum=1.317;SOR=0.425;VQSLOD=5.32;culprit=FS GT:AD:DP:GQ:PL 0/1:10,7:17:99:248,0,336 -chr6 49956510 . C T 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50045305 rs1324514 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50064359 rs9395549 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50087752 rs6458721 A C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50155014 . T A 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:29:40,0,29 -chr6 50155159 rs700005 A C 44.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.37;SOR=0.693;VQSLOD=8.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:72,6,0 -chr6 50158759 rs142079970 G GT 21.73 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.87;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:58,6,0 -chr6 50164244 rs9369936 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50169217 rs148924218 C CT 19.75 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=9.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:56,6,0 -chr6 50197539 rs6910805 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50222518 rs1340844 T C 62.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.92;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 50225593 rs9349526 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50230041 rs1596084 G C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50230068 rs7756066 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50231408 rs6903689 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50261294 rs2792835 T C 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=9.19;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 50265655 rs5876165 GA G 21.73 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=10.87;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:58,6,0 -chr6 50294995 rs10637978 A ATAATT 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.39;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 50298895 rs7775569 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50325057 rs2131281 G A 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=9.10;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 50362460 rs7745382 C A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50364398 rs6930590 G T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50366720 rs7738992 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50650700 rs537362 G C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50805942 rs2817404 T G 938.77 PASS AC=2;AF=1.00;AN=2;DB;DP=23;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.99;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.85;SOR=6.358;VQSLOD=6.90;culprit=FS GT:AD:DP:GQ:PL 1/1:0,23:23:69:967,69,0 -chr6 50810497 rs1569778 T C 85.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.43;SOR=2.833;VQSLOD=7.71;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:113,9,0 -chr6 50811241 rs2982621 T A 306.78 PASS AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.09;SOR=4.615;VQSLOD=5.67;culprit=FS GT:AD:DP:GQ:PL 1/1:0,9:9:27:335,27,0 -chr6 50812003 rs35732696 TA T 11.99 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=4.00;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:48,6,0 -chr6 50824804 rs2817423 T A 1009.77 PASS AC=2;AF=1.00;AN=2;DB;DP=27;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.72;SOR=6.666;VQSLOD=5.96;culprit=FS GT:AD:DP:GQ:PL 1/1:0,27:27:81:1038,81,0 -chr6 50866066 rs11754505 C T 130.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.51;SOR=1.609;VQSLOD=7.49;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:158,12,0 -chr6 50880250 rs61678343 C CT 116.87 PASS AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.73;MQ0=0;QD=16.70;SOR=3.611;VQSLOD=5.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:154,15,0 -chr6 50886019 rs75756982 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.50;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 50966615 rs557411 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51003728 rs140549964 C A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51003757 . T A 62.74 PASS AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.51;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51003762 rs145721769 T A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.99;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51162298 rs1409888 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51171408 rs1327265 G A 95.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=1.179;VQSLOD=9.33;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:123,9,0 -chr6 51173538 rs2256042 G A 107.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.75;SOR=1.179;VQSLOD=8.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 51173541 rs2256041 A G 107.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.80;SOR=1.179;VQSLOD=8.71;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 51199224 rs2796913 T C 136.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.38;SOR=1.981;VQSLOD=6.30;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:165,15,0 -chr6 51274751 . CTT C 59.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.550;ClippingRankSum=1.300;DP=11;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.10;MQ0=0;MQRankSum=-0.937;QD=5.43;ReadPosRankSum=0.550;SOR=0.223;VQSLOD=4.67;culprit=FS GT:AD:DP:GQ:PL 0/1:3,4:7:51:97,0,51 -chr6 51317602 rs9367432 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.44;MQ0=0;QD=7.26;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51329696 rs3928895 G C 93.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.09;SOR=2.833;VQSLOD=8.17;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:121,9,0 -chr6 51339492 rs4090367 T G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51434479 rs4997737 A G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.32;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51434483 rs181171044 A T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.26;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51446475 rs2495854 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51492046 rs9474033 T G 2499.77 PASS AC=2;AF=1.00;AN=2;DB;DP=62;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.45;SOR=8.287;VQSLOD=5.75;culprit=FS GT:AD:DP:GQ:PL 1/1:0,62:62:99:2528,187,0 -chr6 51492164 rs9370040 T A 258.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.68;SOR=4.174;VQSLOD=6.27;culprit=FS GT:AD:DP:GQ:PL 1/1:0,7:7:21:287,21,0 -chr6 51503597 . C CAAA 667.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.313;ClippingRankSum=-1.388;DP=300;FS=6.792;MLEAC=1;MLEAF=0.500;MQ=49.95;MQ0=0;MQRankSum=-2.762;NEGATIVE_TRAIN_SITE;QD=2.23;ReadPosRankSum=-2.418;SOR=0.016;VQSLOD=-2.167e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:77,45:122:99:705,0,1544 -chr6 51512707 rs2580009 T C 944.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.11;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.22;SOR=6.593;VQSLOD=5.86;culprit=FS GT:AD:DP:GQ:PL 1/1:0,26:26:78:973,78,0 -chr6 51521787 . C A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51523739 rs115072237 T C 6637.77 PASS AC=2;AF=1.00;AN=2;DB;DP=176;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.68;SOR=2.371;VQSLOD=5.00;culprit=FS GT:AD:DP:GQ:PL 1/1:0,175:175:99:6666,526,0 -chr6 51551346 rs557398 T C 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=9.05;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 51590078 rs1326610 T C 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.76;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 51604677 . C T 956.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.698;ClippingRankSum=-0.058;DP=66;FS=6.929;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.341;QD=14.50;ReadPosRankSum=1.938;SOR=0.066;VQSLOD=0.460;culprit=FS GT:AD:DP:GQ:PL 0/1:36,30:66:99:985,0,1262 -chr6 51606225 rs142928645 C T 114.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=-1.380;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.380;POSITIVE_TRAIN_SITE;QD=19.13;ReadPosRankSum=0.720;SOR=1.329;VQSLOD=4.76;culprit=FS GT:AD:DP:GQ:PL 0/1:2,4:6:59:143,0,59 -chr6 51611733 rs200125913 A C 194.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.113;ClippingRankSum=1.133;DB;DP=24;FS=9.938;MLEAC=1;MLEAF=0.500;MQ=56.04;MQ0=0;MQRankSum=-0.153;NEGATIVE_TRAIN_SITE;QD=8.12;ReadPosRankSum=0.643;SOR=3.990;VQSLOD=-1.655e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:8,16:24:99:223,0,155 -chr6 51617800 rs1326607 A G 332.77 PASS AC=2;AF=1.00;AN=2;DB;DP=10;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.28;SOR=4.804;VQSLOD=6.82;culprit=FS GT:AD:DP:GQ:PL 1/1:0,10:10:30:361,30,0 -chr6 51634407 . T C 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51640751 rs3920621 C G 1527.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.616;ClippingRankSum=-0.475;DB;DP=114;FS=5.314;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-1.120;POSITIVE_TRAIN_SITE;QD=13.40;ReadPosRankSum=-0.393;SOR=0.217;VQSLOD=1.32;culprit=FS GT:AD:DP:GQ:PL 0/1:63,49:112:99:1556,0,2311 -chr6 51649062 rs11435548 G GT 58.25 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.42;SOR=1.179;VQSLOD=7.95;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:95,9,0 -chr6 51649079 rs4715232 A G 59.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=7.40;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 51652585 rs1326561 A G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=7.54;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51652595 rs1326562 T G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.18;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51655796 rs6904634 T C 99.28 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.93;SOR=2.303;VQSLOD=6.99;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:9:127,9,0 -chr6 51655803 rs6924716 C T 99.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.09;SOR=2.833;VQSLOD=7.69;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:127,9,0 -chr6 51656236 rs7765455 G T 1483.77 PASS AC=2;AF=1.00;AN=2;DB;DP=40;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.49;SOR=3.611;VQSLOD=5.62;culprit=FS GT:AD:DP:GQ:PL 1/1:0,40:40:99:1512,120,0 -chr6 51656388 rs4715233 A G 93.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.09;SOR=2.833;VQSLOD=8.93;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:121,9,0 -chr6 51664791 rs1980834 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51664816 rs2148459 T G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51671321 rs1326584 T A 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=7.93;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 51671350 rs4470847 C G 66.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.09;SOR=1.179;VQSLOD=9.01;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:94,9,0 -chr6 51673939 rs1326588 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51706167 rs10648630 C CCCTTT 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.90;SOR=0.693;VQSLOD=8.28;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51712492 rs9370067 A T 1705.77 PASS AC=2;AF=1.00;AN=2;DB;DP=42;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.14;SOR=7.523;VQSLOD=6.66;culprit=FS GT:AD:DP:GQ:PL 1/1:0,42:42:99:1734,126,0 -chr6 51718857 rs1831015 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51720838 rs9349603 T C 7371.77 PASS AC=2;AF=1.00;AN=2;DB;DP=189;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.82;SOR=2.858;VQSLOD=4.99;culprit=FS GT:AD:DP:GQ:PL 1/1:0,185:185:99:7400,557,0 -chr6 51720872 rs7452724 A G 6199.77 PASS AC=2;AF=1.00;AN=2;DB;DP=161;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.66;SOR=3.188;VQSLOD=6.56;culprit=FS GT:AD:DP:GQ:PL 1/1:0,161:161:99:6228,484,0 -chr6 51723015 rs9370074 G A 50.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=2.303;VQSLOD=7.56;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 51732598 rs9382043 G A 2712.77 PASS AC=2;AF=1.00;AN=2;DB;DP=74;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.50;SOR=3.026;VQSLOD=5.85;culprit=FS GT:AD:DP:GQ:PL 1/1:0,74:74:99:2741,222,0 -chr6 51732628 rs9382044 G A 3330.77 PASS AC=2;AF=1.00;AN=2;DB;DP=89;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.74;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.80;SOR=2.276;VQSLOD=6.28;culprit=FS GT:AD:DP:GQ:PL 1/1:0,89:89:99:3359,267,0 -chr6 51735261 rs982874 G T 2752.77 PASS AC=2;AF=1.00;AN=2;DB;DP=73;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.49;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.40;SOR=4.558;VQSLOD=6.00;culprit=FS GT:AD:DP:GQ:PL 1/1:0,73:73:99:2781,220,0 -chr6 51735613 rs2064871 T C 314.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.95;SOR=4.407;VQSLOD=6.77;culprit=FS GT:AD:DP:GQ:PL 1/1:0,8:8:24:343,24,0 -chr6 51747589 rs6458801 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51750563 rs4711985 A T 498.77 PASS AC=2;AF=1.00;AN=2;DB;DP=13;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.32;SOR=5.283;VQSLOD=6.36;culprit=FS GT:AD:DP:GQ:PL 1/1:0,13:13:39:527,39,0 -chr6 51757014 rs1321516 C T 63.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.44;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 51768630 rs141063789 CATATAT C 229.77 PASS AC=2;AF=1.00;AN=2;DB;DP=22;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.71;MQ0=0;POSITIVE_TRAIN_SITE;QD=10.44;SOR=2.303;VQSLOD=6.39;culprit=FS GT:AD:DP:GQ:PL 1/1:0,6:6:20:267,20,0 -chr6 51791091 rs4711990 G T 63.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.23;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 51793425 rs5876244 C CA 44.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=0.693;VQSLOD=8.40;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 51796751 rs3857602 G A 89.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.76;SOR=1.179;VQSLOD=5.58;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:117,9,0 -chr6 51798753 rs1266888 G A 308.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.90;SOR=4.407;VQSLOD=6.30;culprit=FS GT:AD:DP:GQ:PL 1/1:0,8:8:24:337,24,0 -chr6 51798760 rs1884953 T A 94.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=-0.365;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.365;POSITIVE_TRAIN_SITE;QD=9.48;ReadPosRankSum=-0.365;SOR=0.412;VQSLOD=6.15;culprit=FS GT:AD:DP:GQ:PL 0/1:6,4:10:99:123,0,204 -chr6 51799166 rs1266889 T C 1497.77 PASS AC=2;AF=1.00;AN=2;DB;DP=38;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.26;SOR=4.977;VQSLOD=5.51;culprit=FS GT:AD:DP:GQ:PL 1/1:0,37:37:99:1526,111,0 -chr6 51800445 rs1266890 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51814216 rs4715264 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.34;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51814217 rs1266913 A G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.56;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 51844368 rs2435324 A G 48.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=8.63;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 51856374 rs9463746 A G 45.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=2.303;VQSLOD=8.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 -chr6 51875250 rs2435322 A C 4902.77 PASS AC=2;AF=1.00;AN=2;DB;DP=132;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.68;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.79;SOR=1.170;VQSLOD=5.57;culprit=FS GT:AD:DP:GQ:PL 1/1:0,130:130:99:4931,391,0 -chr6 51882075 rs9349614 C G 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.067;ClippingRankSum=0.572;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.589;QD=3.31;ReadPosRankSum=0.572;SOR=0.169 GT:AD:DP:GQ:PL 0/1:6,2:8:58:58,0,201 -chr6 51889483 rs45517932 G A 1402.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.623;ClippingRankSum=-0.441;DB;DP=91;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.758;QD=15.42;ReadPosRankSum=0.099;SOR=0.684;VQSLOD=3.39;culprit=FS GT:AD:DP:GQ:PL 0/1:47,44:91:99:1431,0,1559 -chr6 51890823 rs9296669 G A 908.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.796;ClippingRankSum=-1.279;DB;DP=60;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=0.614;POSITIVE_TRAIN_SITE;QD=15.15;ReadPosRankSum=0.052;SOR=0.575;VQSLOD=5.85;culprit=FS GT:AD:DP:GQ:PL 0/1:30,30:60:99:937,0,937 -chr6 51891011 rs2499480 T C 1469.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.480;ClippingRankSum=1.669;DB;DP=99;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=-0.671;POSITIVE_TRAIN_SITE;QD=14.85;ReadPosRankSum=0.425;SOR=0.787;VQSLOD=5.12;culprit=FS GT:AD:DP:GQ:PL 0/1:54,45:99:99:1498,0,1703 -chr6 51913240 rs10948667 G A 2227.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.872;ClippingRankSum=0.978;DB;DP=133;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.127;POSITIVE_TRAIN_SITE;QD=16.75;ReadPosRankSum=0.314;SOR=0.691;VQSLOD=4.01;culprit=FS GT:AD:DP:GQ:PL 0/1:61,72:133:99:2256,0,2006 -chr6 51914898 rs9395759 T C 962.77 PASS AC=2;AF=1.00;AN=2;DB;DP=27;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.65;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.45;SOR=5.211;VQSLOD=6.92;culprit=FS GT:AD:DP:GQ:PL 1/1:0,27:27:81:991,81,0 -chr6 51914956 rs9370096 G A 738.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.924;ClippingRankSum=-1.239;DB;DP=57;FS=1.721;MLEAC=1;MLEAF=0.500;MQ=53.16;MQ0=0;MQRankSum=-2.997;POSITIVE_TRAIN_SITE;QD=12.96;ReadPosRankSum=0.567;SOR=1.274;VQSLOD=0.740;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:30,27:57:99:767,0,838 -chr6 51917550 rs1896983 G A 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.73;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 51923569 rs56342114 CTCTA C 188.84 PASS AC=2;AF=1.00;AN=2;DB;DP=12;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.74;SOR=3.611;VQSLOD=5.56;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:16:226,16,0 -chr6 51924774 rs1896976 A G 11214.77 PASS AC=2;AF=1.00;AN=2;DB;DP=307;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.86;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.73;SOR=0.923;VQSLOD=3.90;culprit=FS GT:AD:DP:GQ:PL 1/1:0,306:306:99:11243,918,0 -chr6 51927683 rs13198604 T C 130.79 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=21.80;ReadPosRankSum=0.736;SOR=0.941;VQSLOD=5.66;culprit=FS GT:AD:DP:GQ:PL 0/1:1,5:6:22:159,0,22 -chr6 51930886 rs5876252 T TA 1123.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.558;ClippingRankSum=0.596;DB;DP=98;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=0;MQRankSum=0.066;POSITIVE_TRAIN_SITE;QD=11.47;ReadPosRankSum=0.047;SOR=1.571;VQSLOD=5.61;culprit=FS GT:AD:DP:GQ:PL 0/1:14,49:63:99:1161,0,109 -chr6 51935061 rs4711996 T G 632.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.75;SOR=5.670;VQSLOD=6.32;culprit=FS GT:AD:DP:GQ:PL 1/1:0,16:16:48:661,48,0 -chr6 51935747 rs17576809 C T 1555.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.681;ClippingRankSum=0.579;DB;DP=78;FS=1.884;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.207;POSITIVE_TRAIN_SITE;QD=19.95;ReadPosRankSum=2.282;SOR=1.437;VQSLOD=1.66;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:34,44:78:99:1584,0,1003 -chr6 51936846 rs3936986 T C 1197.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.520;ClippingRankSum=2.065;DB;DP=65;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.165;POSITIVE_TRAIN_SITE;QD=18.43;ReadPosRankSum=-0.310;SOR=0.499;VQSLOD=5.41;culprit=FS GT:AD:DP:GQ:PL 0/1:29,36:65:99:1226,0,894 -chr6 51938242 rs9474140 A G 2915.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=5.879;ClippingRankSum=-1.660;DB;DP=204;FS=1.266;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=0.616;POSITIVE_TRAIN_SITE;QD=14.29;ReadPosRankSum=0.116;SOR=0.846;VQSLOD=2.35;culprit=DP GT:AD:DP:GQ:PL 0/1:112,92:204:99:2944,0,3367 -chr6 51944847 rs1892274 T C 1304.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.941;ClippingRankSum=0.488;DB;DP=91;FS=6.922;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=-0.933;POSITIVE_TRAIN_SITE;QD=14.34;ReadPosRankSum=0.242;SOR=2.140;VQSLOD=2.08;culprit=FS GT:AD:DP:GQ:PL 0/1:45,46:91:99:1333,0,1431 -chr6 51946893 rs6458806 T C 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=8.64;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 51947237 rs9474143 G A 5131.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.494;ClippingRankSum=0.221;DB;DP=273;FS=2.813;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.398;POSITIVE_TRAIN_SITE;QD=18.80;ReadPosRankSum=1.871;SOR=0.538;VQSLOD=1.29;culprit=DP GT:AD:DP:GQ:PL 0/1:114,158:272:99:5160,0,3305 -chr6 51949862 rs9370097 A G 953.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.068;ClippingRankSum=-1.115;DB;DP=65;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.363;POSITIVE_TRAIN_SITE;QD=14.67;ReadPosRankSum=-0.917;SOR=0.505;VQSLOD=5.49;culprit=FS GT:AD:DP:GQ:PL 0/1:36,29:65:99:982,0,1231 -chr6 51953191 rs6905678 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51963443 rs6914462 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 51971195 rs3997006 T C 91.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=2.833;VQSLOD=7.51;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:119,9,0 -chr6 51997155 rs1892278 A C 327.78 PASS AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.88;SOR=3.056;VQSLOD=5.59;culprit=FS GT:AD:DP:GQ:PL 1/1:0,9:9:27:356,27,0 -chr6 52054249 rs7747909 G A 105.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.421;ClippingRankSum=0.922;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.017;POSITIVE_TRAIN_SITE;QD=13.22;ReadPosRankSum=0.000;SOR=0.693;VQSLOD=4.45;culprit=FS GT:AD:DP:GQ:PL 0/1:4,4:8:99:134,0,134 -chr6 52061133 rs11962054 A G 16.63 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=16.63;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:43,3,0 -chr6 52064989 rs11755816 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52065009 rs11751159 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52073500 rs4464776 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52075816 rs2397079 A G 59.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=9.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 52085748 rs591274 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52111808 rs761167 C T 630.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.571;ClippingRankSum=-0.018;DB;DP=33;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.792;POSITIVE_TRAIN_SITE;QD=19.11;ReadPosRankSum=0.534;SOR=0.743;VQSLOD=5.64;culprit=FS GT:AD:DP:GQ:PL 0/1:13,20:33:99:659,0,402 -chr6 52117224 rs604952 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52129484 rs2230240 C T 3990.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.023;ClippingRankSum=-0.723;DB;DP=236;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.012;POSITIVE_TRAIN_SITE;QD=16.91;ReadPosRankSum=2.682;SOR=0.712;VQSLOD=1.85;culprit=FS GT:AD:DP:GQ:PL 0/1:105,131:236:99:4019,0,2992 -chr6 52129667 rs2307326 G A 917.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.356;ClippingRankSum=-0.312;DB;DP=53;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.791;POSITIVE_TRAIN_SITE;QD=17.32;ReadPosRankSum=-2.147;SOR=0.808;VQSLOD=3.93;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:25,28:53:99:946,0,873 -chr6 52130745 rs6925229 T C 162.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.139;ClippingRankSum=1.898;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.488;POSITIVE_TRAIN_SITE;QD=10.17;ReadPosRankSum=0.597;SOR=0.340;VQSLOD=6.23;culprit=FS GT:AD:DP:GQ:PL 0/1:10,6:16:99:191,0,354 -chr6 52131254 rs10807441 C T 1383.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.953;ClippingRankSum=0.770;DB;DP=83;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.223;POSITIVE_TRAIN_SITE;QD=16.67;ReadPosRankSum=0.269;SOR=1.534;VQSLOD=5.05;culprit=FS GT:AD:DP:GQ:PL 0/1:43,40:83:99:1412,0,1442 -chr6 52137313 rs12207056 C T 464.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.684;ClippingRankSum=-0.306;DB;DP=33;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=47.56;MQ0=0;MQRankSum=-0.162;POSITIVE_TRAIN_SITE;QD=14.08;ReadPosRankSum=1.207;SOR=1.609;VQSLOD=5.72;culprit=FS GT:AD:DP:GQ:PL 0/1:17,16:33:99:493,0,518 -chr6 52138441 rs6918669 G A 286.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.355;ClippingRankSum=-0.442;DB;DP=18;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=15.93;ReadPosRankSum=0.971;SOR=1.781;VQSLOD=6.47;culprit=FS GT:AD:DP:GQ:PL 0/1:9,9:18:99:315,0,267 -chr6 52141670 rs3765446 A T 142.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.635;ClippingRankSum=1.000;DB;DP=12;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.134;POSITIVE_TRAIN_SITE;QD=11.90;ReadPosRankSum=0.135;SOR=1.371;VQSLOD=6.12;culprit=FS GT:AD:DP:GQ:PL 0/1:7,5:12:99:171,0,247 -chr6 52142092 rs2307325 C T 222.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.092;ClippingRankSum=0.092;DB;DP=24;FS=1.999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.276;POSITIVE_TRAIN_SITE;QD=9.28;ReadPosRankSum=0.704;SOR=1.214;VQSLOD=2.73;culprit=QD GT:AD:DP:GQ:PL 0/1:16,8:24:99:251,0,540 -chr6 52142582 rs13191372 G A 424.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.394;ClippingRankSum=0.496;DB;DP=31;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=0;MQRankSum=0.695;POSITIVE_TRAIN_SITE;QD=13.70;ReadPosRankSum=1.409;SOR=0.527;VQSLOD=5.12;culprit=FS GT:AD:DP:GQ:PL 0/1:17,14:31:99:453,0,593 -chr6 52143987 rs2076510 C T 232.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.780;ClippingRankSum=-0.625;DB;DP=17;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.241;POSITIVE_TRAIN_SITE;QD=13.69;ReadPosRankSum=1.973;SOR=0.593;VQSLOD=5.87;culprit=FS GT:AD:DP:GQ:PL 0/1:9,8:17:99:261,0,314 -chr6 52144081 rs2073036 T C 952.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;ClippingRankSum=-0.724;DB;DP=63;FS=1.092;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.193;POSITIVE_TRAIN_SITE;QD=15.12;ReadPosRankSum=0.145;SOR=0.485;VQSLOD=2.82;culprit=FS GT:AD:DP:GQ:PL 0/1:29,34:63:99:981,0,911 -chr6 52147271 rs7756989 T C 20.80 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;ClippingRankSum=1.380;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.720;QD=3.47;ReadPosRankSum=0.720;SOR=0.693 GT:AD:DP:GQ:PL 0/1:4,2:6:49:49,0,109 -chr6 52147363 rs12202495 A G 191.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.279;ClippingRankSum=0.579;DB;DP=20;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.193;POSITIVE_TRAIN_SITE;QD=9.59;ReadPosRankSum=1.042;SOR=0.392;VQSLOD=5.45;culprit=FS GT:AD:DP:GQ:PL 0/1:12,8:20:99:220,0,424 -chr6 52147692 rs2307322 T A 893.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=5.042;ClippingRankSum=0.160;DB;DP=47;FS=9.107;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.460;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=19.02;ReadPosRankSum=3.166;SOR=2.472;VQSLOD=0.472;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:22,25:47:99:922,0,588 -chr6 52148465 rs9474192 T G 63.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.21;culprit=QD GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 52217185 rs9395785 C G 142.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-0.922;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.495;POSITIVE_TRAIN_SITE;QD=20.40;ReadPosRankSum=0.922;SOR=1.609;VQSLOD=5.94;culprit=FS GT:AD:DP:GQ:PL 0/1:2,5:7:66:171,0,66 -chr6 52240487 rs6458837 G A 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=7.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 52245945 rs71794438 CA C 38.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=2.303;VQSLOD=7.53;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 52257835 rs669893 A G 17.61 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=17.61;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:44,3,0 -chr6 52257856 rs526553 G C 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.49;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 52267967 rs76408349 A C 39.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=1.231;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.21;MQ0=0;MQRankSum=1.231;POSITIVE_TRAIN_SITE;QD=7.95;ReadPosRankSum=-0.358;SOR=0.446;VQSLOD=5.70;culprit=QD GT:AD:DP:GQ:PL 0/1:3,2:5:68:68,0,92 -chr6 52268008 rs3748066 T G 117.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.495;ClippingRankSum=0.198;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.03;MQ0=0;MQRankSum=-0.922;POSITIVE_TRAIN_SITE;QD=16.82;ReadPosRankSum=-0.922;SOR=0.527;VQSLOD=6.33;culprit=FS GT:AD:DP:GQ:PL 0/1:2,5:7:62:146,0,62 -chr6 52268086 rs146353145 C T 319.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.458;ClippingRankSum=-0.387;DB;DP=21;FS=3.222;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=0;MQRankSum=-0.810;QD=15.23;ReadPosRankSum=0.599;SOR=1.911;VQSLOD=1.55;culprit=FS GT:AD:DP:GQ:PL 0/1:10,11:21:99:348,0,301 -chr6 52268890 rs17591381 G A 546.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.060;ClippingRankSum=0.774;DB;DP=49;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.58;MQ0=0;MQRankSum=1.035;POSITIVE_TRAIN_SITE;QD=11.16;ReadPosRankSum=0.794;SOR=0.712;VQSLOD=5.57;culprit=FS GT:AD:DP:GQ:PL 0/1:27,22:49:99:575,0,819 -chr6 52269199 rs3799272 T C 59.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=9.07;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 52296461 rs1840169 G C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52319251 rs614570 C T 274.18 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.751;ClippingRankSum=0.751;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.751;POSITIVE_TRAIN_SITE;QD=30.46;ReadPosRankSum=0.751;SOR=3.056;VQSLOD=5.38;culprit=FS GT:AD:DP:GQ:PL 0/1:1,8:9:10:302,0,10 -chr6 52355206 rs2273120 T C 1095.77 PASS AC=2;AF=1.00;AN=2;DB;DP=30;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.61;SOR=5.353;VQSLOD=6.99;culprit=FS GT:AD:DP:GQ:PL 1/1:0,29:29:87:1124,87,0 -chr6 52357260 rs7757370 C A 601.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.84;SOR=5.670;VQSLOD=6.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,16:16:48:630,48,0 -chr6 52367845 rs3032 C T 381.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.028;ClippingRankSum=0.927;DB;DP=24;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=0.695;POSITIVE_TRAIN_SITE;QD=15.91;ReadPosRankSum=-0.348;SOR=0.859;VQSLOD=5.92;culprit=FS GT:AD:DP:GQ:PL 0/1:11,13:24:99:410,0,338 -chr6 52370939 rs9688915 G A 1148.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.520;ClippingRankSum=1.052;DB;DP=64;FS=1.426;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.175;POSITIVE_TRAIN_SITE;QD=17.95;ReadPosRankSum=0.836;SOR=1.212;VQSLOD=2.70;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:29,35:64:99:1177,0,853 -chr6 52380641 rs941968 C T 424.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.390;ClippingRankSum=-1.102;DB;DP=30;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.395;POSITIVE_TRAIN_SITE;QD=14.16;ReadPosRankSum=0.603;SOR=0.576;VQSLOD=5.79;culprit=FS GT:AD:DP:GQ:PL 0/1:16,14:30:99:453,0,559 -chr6 52381728 rs6917085 A T 86.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=21.69;ReadPosRankSum=-0.727;SOR=1.609;VQSLOD=6.10;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:32:115,0,32 -chr6 52425189 rs7744675 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52433894 rs55959984 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52451301 . A G 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52453985 rs9370135 T A 42.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.26;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.69;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:30:71,0,30 -chr6 52469904 rs9463802 A G 49.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=9.20;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 52475696 . C A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52483058 rs11755043 C A 49.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=8.10;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 52538160 rs55704840 A AG 38.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=0.693;VQSLOD=8.83;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 52538171 rs7746344 A G 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.58;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 52538198 rs9349638 T A 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.37;SOR=0.693;VQSLOD=7.10;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 52538242 rs9349639 T G 50.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=0.693;VQSLOD=7.79;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 52538390 rs9349640 T C 45.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=0.693;VQSLOD=8.54;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 -chr6 52541811 rs13211066 G A 2092.77 PASS AC=2;AF=1.00;AN=2;DB;DP=52;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.36;SOR=7.941;VQSLOD=6.16;culprit=FS GT:AD:DP:GQ:PL 1/1:0,52:52:99:2121,157,0 -chr6 52546789 rs2281484 C T 1421.77 PASS AC=2;AF=1.00;AN=2;DB;DP=38;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.25;SOR=7.328;VQSLOD=7.46;culprit=FS GT:AD:DP:GQ:PL 1/1:0,38:38:99:1450,114,0 -chr6 52553436 rs9382133 C T 766.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.752;ClippingRankSum=0.060;DB;DP=45;FS=4.452;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=0.370;POSITIVE_TRAIN_SITE;QD=17.04;ReadPosRankSum=0.418;SOR=1.118;VQSLOD=2.96;culprit=FS GT:AD:DP:GQ:PL 0/1:18,26:44:99:795,0,532 -chr6 52565427 rs4637643 T G 63.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=8.30;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 52568775 rs6909894 G C 181.90 PASS AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.32;SOR=1.981;VQSLOD=6.47;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:210,15,0 -chr6 52568848 rs36098646 G GA 25.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=62.65;MQ0=0;MQRankSum=0.727;QD=6.49;ReadPosRankSum=0.727;SOR=0.916 GT:AD:DP:GQ:PL 0/1:1,3:4:13:63,0,13 -chr6 52615371 rs199546282 T G 302.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-7.160;ClippingRankSum=-0.230;DB;DP=163;FS=296.910;MLEAC=1;MLEAF=0.500;MQ=54.98;MQ0=0;MQRankSum=-0.947;QD=1.86;ReadPosRankSum=-4.824;SOR=8.189;VQSLOD=-1.995e+02;culprit=FS GT:AD:DP:GQ:PL 0/1:103,59:162:99:331,0,2945 -chr6 52616633 rs72934249 C T 667.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.954;ClippingRankSum=0.781;DB;DP=47;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.909;POSITIVE_TRAIN_SITE;QD=14.21;ReadPosRankSum=-0.631;SOR=0.509;VQSLOD=5.18;culprit=FS GT:AD:DP:GQ:PL 0/1:26,21:47:99:696,0,789 -chr6 52617731 rs2180314 C G 6239.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.736;ClippingRankSum=-0.690;DB;DP=405;FS=1.200;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=-0.793;POSITIVE_TRAIN_SITE;QD=15.41;ReadPosRankSum=1.185;SOR=0.583;VQSLOD=1.22;culprit=DP GT:AD:DP:GQ:PL 0/1:207,197:404:99:6268,0,6969 -chr6 52622475 rs2608624 G T 277.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.387;ClippingRankSum=-0.529;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.529;POSITIVE_TRAIN_SITE;QD=17.36;ReadPosRankSum=-1.482;SOR=0.941;VQSLOD=4.88;culprit=FS GT:AD:DP:GQ:PL 0/1:7,9:16:99:306,0,255 -chr6 52622814 rs2254050 C T 889.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=5.466;ClippingRankSum=2.068;DB;DP=50;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.456;POSITIVE_TRAIN_SITE;QD=17.80;ReadPosRankSum=0.651;SOR=0.773;VQSLOD=5.34;culprit=FS GT:AD:DP:GQ:PL 0/1:24,26:50:99:918,0,713 -chr6 52630153 rs6458868 C T 560.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.030;ClippingRankSum=-0.430;DB;DP=42;FS=1.283;MLEAC=1;MLEAF=0.500;MQ=56.17;MQ0=0;MQRankSum=0.483;POSITIVE_TRAIN_SITE;QD=13.35;ReadPosRankSum=2.308;SOR=1.064;VQSLOD=2.33;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:21,20:41:99:589,0,560 -chr6 52630269 rs6458869 C A 534.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.861;ClippingRankSum=-1.139;DB;DP=26;FS=1.757;MLEAC=1;MLEAF=0.500;MQ=49.59;MQ0=0;MQRankSum=-2.083;POSITIVE_TRAIN_SITE;QD=20.57;ReadPosRankSum=-0.583;SOR=0.346;VQSLOD=1.61;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:8,18:26:99:563,0,197 -chr6 52631188 rs2749029 A G 696.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.911;ClippingRankSum=0.581;DB;DP=58;FS=2.243;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-0.722;POSITIVE_TRAIN_SITE;QD=12.01;ReadPosRankSum=0.581;SOR=0.416;VQSLOD=2.99;culprit=QD GT:AD:DP:GQ:PL 0/1:33,25:58:99:725,0,1078 -chr6 52655827 rs6904269 G A 49.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=9.25;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 52657321 rs4147615 T C 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=9.21;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 52658962 rs1051775 T C 16388.77 VQSRTrancheSNP99.00to99.90 AC=2;AF=1.00;AN=2;BaseQRankSum=1.724;ClippingRankSum=-0.564;DB;DP=430;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.91;MQ0=0;MQRankSum=0.177;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=26.20;ReadPosRankSum=0.878;SOR=0.736;VQSLOD=-8.417e-01;culprit=DP GT:AD:DP:GQ:PL 1/1:1,429:430:99:16417,1283,0 -chr6 52660828 rs2894803 C A 2866.77 PASS AC=2;AF=1.00;AN=2;DB;DP=74;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.91;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.82;SOR=8.608;VQSLOD=6.77;culprit=FS GT:AD:DP:GQ:PL 1/1:0,73:73:99:2895,220,0 -chr6 52661267 . ATATATATATATATATATATATGTGTG A 235.79 PASS AC=2;AF=1.00;AN=2;DP=21;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.56;MQ0=0;QD=11.23;SOR=3.912;VQSLOD=4.84;culprit=FS GT:AD:DP:GQ:PL 1/1:0,6:6:19:273,19,0 -chr6 52662263 rs2397106 C T 1326.77 PASS AC=2;AF=1.00;AN=2;DB;DP=39;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=34.02;SOR=5.892;VQSLOD=5.23;culprit=FS GT:AD:DP:GQ:PL 1/1:0,38:38:99:1355,114,0 -chr6 52662568 rs139503836 G A 365.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.392;ClippingRankSum=-0.198;DB;DP=36;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=0;MQRankSum=-1.778;QD=10.16;ReadPosRankSum=1.120;SOR=0.293;VQSLOD=2.34;culprit=FS GT:AD:DP:GQ:PL 0/1:23,13:36:99:394,0,797 -chr6 52663705 rs9349644 C T 48.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=7.95;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 52663813 rs10948722 A G 801.77 PASS AC=2;AF=1.00;AN=2;DB;DP=20;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.84;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.88;SOR=6.091;VQSLOD=6.69;culprit=FS GT:AD:DP:GQ:PL 1/1:0,20:20:60:830,60,0 -chr6 52664133 . T C 1090.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.013;ClippingRankSum=-0.873;DP=57;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.328;QD=19.14;ReadPosRankSum=0.377;SOR=0.285;VQSLOD=3.89;culprit=FS GT:AD:DP:GQ:PL 0/1:26,31:57:99:1119,0,874 -chr6 52670630 rs10807454 A C 691.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.81;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.23;SOR=3.258;VQSLOD=6.57;culprit=FS GT:AD:DP:GQ:PL 1/1:0,16:16:48:720,48,0 -chr6 52670633 rs62412861 A G 725.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.81;MQ0=0;QD=24.12;SOR=3.258;VQSLOD=4.49;culprit=FS GT:AD:DP:GQ:PL 1/1:0,16:16:51:754,51,0 -chr6 52670639 rs62412870 C T 680.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.44;MQ0=0;QD=29.35;SOR=3.258;VQSLOD=4.94;culprit=FS GT:AD:DP:GQ:PL 1/1:0,16:16:48:709,48,0 -chr6 52677230 rs5876288 G GA 2040.73 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-0.420;ClippingRankSum=0.166;DB;DP=129;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=0.381;POSITIVE_TRAIN_SITE;QD=15.82;ReadPosRankSum=-0.674;SOR=1.636;VQSLOD=4.43;culprit=FS GT:AD:DP:GQ:PL 1/1:6,81:87:99:2070,156,0 -chr6 52678337 rs6458873 G T 1706.77 PASS AC=2;AF=1.00;AN=2;DB;DP=44;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.61;SOR=5.330;VQSLOD=6.87;culprit=FS GT:AD:DP:GQ:PL 1/1:0,44:44:99:1735,132,0 -chr6 52678463 rs6458874 C T 360.77 PASS AC=2;AF=1.00;AN=2;DB;DP=10;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.66;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.20;SOR=4.804;VQSLOD=6.59;culprit=FS GT:AD:DP:GQ:PL 1/1:0,10:10:30:389,30,0 -chr6 52678500 rs6458875 C G 82.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.43;SOR=2.833;VQSLOD=8.62;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:110,9,0 -chr6 52688905 rs2983232 G T 13.72 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=13.72;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 -chr6 52694086 rs4311507 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52695461 rs10948726 G T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.50;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52697601 rs55815585 T G 3617.77 PASS AC=2;AF=1.00;AN=2;DB;DP=94;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.68;SOR=2.354;VQSLOD=5.15;culprit=FS GT:AD:DP:GQ:PL 1/1:0,92:92:99:3646,277,0 -chr6 52697825 rs4715345 A C 5351.77 PASS AC=2;AF=1.00;AN=2;DB;DP=123;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.29;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.62;SOR=2.226;VQSLOD=5.04;culprit=FS GT:AD:DP:GQ:PL 1/1:0,122:122:99:5380,367,0 -chr6 52697834 rs4715346 C A 5365.77 PASS AC=2;AF=1.00;AN=2;DB;DP=120;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.25;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.36;SOR=2.507;VQSLOD=5.69;culprit=FS GT:AD:DP:GQ:PL 1/1:0,120:120:99:5394,370,0 -chr6 52697890 rs4715347 C T 2514.77 PASS AC=2;AF=1.00;AN=2;DB;DP=66;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.18;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.91;SOR=5.042;VQSLOD=6.95;culprit=QD GT:AD:DP:GQ:PL 1/1:0,65:65:99:2543,195,0 -chr6 52698035 rs4715348 A G 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=8.47;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 52698653 rs6458880 C T 131.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.76;SOR=3.258;VQSLOD=7.46;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:159,12,0 -chr6 52698788 rs4712021 T C 3962.77 PASS AC=2;AF=1.00;AN=2;DB;DP=88;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.39;SOR=8.977;VQSLOD=6.17;culprit=FS GT:AD:DP:GQ:PL 1/1:0,88:88:99:3991,271,0 -chr6 52698798 rs4715349 G T 4293.77 PASS AC=2;AF=1.00;AN=2;DB;DP=99;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.88;SOR=9.210;VQSLOD=6.95;culprit=DP GT:AD:DP:GQ:PL 1/1:0,99:99:99:4322,298,0 -chr6 52700920 rs2397117 T C 5074.77 PASS AC=2;AF=1.00;AN=2;DB;DP=131;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.86;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.54;SOR=9.735;VQSLOD=6.59;culprit=FS GT:AD:DP:GQ:PL 1/1:0,129:129:99:5103,388,0 -chr6 52701143 rs2397118 C T 12265.77 PASS AC=2;AF=1.00;AN=2;DB;DP=338;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.80;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.40;SOR=1.526;VQSLOD=2.73;culprit=FS GT:AD:DP:GQ:PL 1/1:0,337:337:99:12294,1013,0 -chr6 52701458 rs2397119 T C 81.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.09;SOR=2.833;VQSLOD=7.99;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:109,9,0 -chr6 52701582 rs62412887 T A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.25;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 52701589 rs2397121 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=7.15;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 52702324 rs4715350 T C 4926.77 PASS AC=2;AF=1.00;AN=2;DB;DP=136;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.30;SOR=3.048;VQSLOD=4.71;culprit=FS GT:AD:DP:GQ:PL 1/1:0,135:135:99:4955,406,0 -chr6 52702529 rs4715351 T C 1973.77 PASS AC=2;AF=1.00;AN=2;DB;DP=48;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.52;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.80;SOR=7.743;VQSLOD=6.84;culprit=FS GT:AD:DP:GQ:PL 1/1:0,47:47:99:2002,141,0 -chr6 52712461 rs9296693 G A 232.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.26;SOR=4.174;VQSLOD=3.81;culprit=FS GT:AD:DP:GQ:PL 1/1:0,7:7:21:261,21,0 -chr6 52712645 rs9296694 C G 4081.77 PASS AC=2;AF=1.00;AN=2;DB;DP=107;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.14;SOR=2.812;VQSLOD=6.01;culprit=FS GT:AD:DP:GQ:PL 1/1:0,107:107:99:4110,322,0 -chr6 52713902 rs62412891 C T 1799.77 PASS AC=2;AF=1.00;AN=2;DB;DP=47;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.94;SOR=3.958;VQSLOD=6.18;culprit=FS GT:AD:DP:GQ:PL 1/1:0,47:47:99:1828,141,0 -chr6 52724654 rs9349647 C T 94.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.43;SOR=2.833;VQSLOD=8.25;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:122,9,0 -chr6 52735179 rs72938158 T A 2626.77 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.785;ClippingRankSum=1.186;DB;DP=68;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=-1.577;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=31.32;ReadPosRankSum=3.323;SOR=5.136;VQSLOD=0.542;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 1/1:4,64:68:99:2655,186,0 -chr6 52743455 rs4715360 T C 2478.77 PASS AC=2;AF=1.00;AN=2;DB;DP=62;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=8.287;VQSLOD=5.41;culprit=FS GT:AD:DP:GQ:PL 1/1:0,62:62:99:2507,187,0 -chr6 52744741 rs13198332 G A 498.77 PASS AC=2;AF=1.00;AN=2;DB;DP=14;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.93;SOR=0.693;VQSLOD=6.43;culprit=FS GT:AD:DP:GQ:PL 1/1:0,14:14:42:527,42,0 -chr6 52746642 rs72940404 G A 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:30:40,0,30 -chr6 52761898 rs2295605 T C 585.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.63;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.46;SOR=5.784;VQSLOD=7.27;culprit=FS GT:AD:DP:GQ:PL 1/1:0,17:17:51:614,51,0 -chr6 52766192 rs6935603 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52767869 rs542113 T A 53.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=8.36;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 52768392 . CA C 63.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.806;ClippingRankSum=-0.832;DP=73;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.10;MQ0=0;MQRankSum=1.360;QD=0.87;ReadPosRankSum=-1.466;SOR=0.111;VQSLOD=2.98;culprit=FS GT:AD:DP:GQ:PL 0/1:42,11:53:99:101,0,838 -chr6 52785560 rs689167 G A 446.77 PASS AC=2;AF=1.00;AN=2;DB;DP=13;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.37;SOR=0.836;VQSLOD=7.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,13:13:39:475,39,0 -chr6 52785580 rs689197 G A 546.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.55;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.17;SOR=0.693;VQSLOD=6.60;culprit=FS GT:AD:DP:GQ:PL 1/1:0,16:16:48:575,48,0 -chr6 52785649 rs581594 G A 388.77 PASS AC=2;AF=1.00;AN=2;DB;DP=11;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.47;SOR=4.804;VQSLOD=6.33;culprit=FS GT:AD:DP:GQ:PL 1/1:0,10:10:30:417,30,0 -chr6 52795274 rs547362 G T 47.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=0.693;VQSLOD=8.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 52802244 rs371403 A G 109.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.26;SOR=1.609;VQSLOD=7.67;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:137,12,0 -chr6 52820382 rs10948733 G A 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.62;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 52835606 rs571672 T C 114.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.51;SOR=3.258;VQSLOD=6.85;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:142,12,0 -chr6 52839185 rs428957 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52843131 rs367836 G T 2227.77 PASS AC=2;AF=1.00;AN=2;DB;DP=54;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.34;SOR=8.015;VQSLOD=7.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,54:54:99:2256,163,0 -chr6 52843477 rs375887 A G 995.77 PASS AC=2;AF=1.00;AN=2;DB;DP=26;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.52;SOR=5.058;VQSLOD=6.33;culprit=FS GT:AD:DP:GQ:PL 1/1:0,25:25:75:1024,75,0 -chr6 52843524 rs543613 T C 344.78 PASS AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.54;SOR=4.615;VQSLOD=4.87;culprit=FS GT:AD:DP:GQ:PL 1/1:0,9:9:27:373,27,0 -chr6 52847150 rs67390777 TA T 38.25 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=66.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=12.75;SOR=2.833;VQSLOD=8.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:75,9,0 -chr6 52847273 rs3831189 T TAC 756.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.167;ClippingRankSum=0.026;DB;DP=33;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=61.26;MQ0=0;MQRankSum=-0.078;POSITIVE_TRAIN_SITE;QD=22.93;ReadPosRankSum=0.544;SOR=2.621;VQSLOD=6.58;culprit=FS GT:AD:DP:GQ:PL 0/1:6,24:30:99:794,0,101 -chr6 52847551 rs316133 G C 3193.77 PASS AC=2;AF=1.00;AN=2;DB;DP=83;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.72;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.28;SOR=2.833;VQSLOD=6.64;culprit=FS GT:AD:DP:GQ:PL 1/1:0,83:83:99:3222,249,0 -chr6 52847682 rs10557482 GGAGA G 232.80 PASS AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=62.36;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=3.912;VQSLOD=6.22;culprit=FS GT:AD:DP:GQ:PL 1/1:0,6:6:18:270,18,0 -chr6 52849146 rs316128 G T 959.77 PASS AC=2;AF=1.00;AN=2;DB;DP=28;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.28;SOR=5.136;VQSLOD=6.09;culprit=FS GT:AD:DP:GQ:PL 1/1:0,26:26:78:988,78,0 -chr6 52849481 . C CT 353.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.178;ClippingRankSum=-1.730;DP=59;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.53;MQ0=0;MQRankSum=-0.663;POSITIVE_TRAIN_SITE;QD=6.00;ReadPosRankSum=-1.275;SOR=1.609;VQSLOD=5.78;culprit=FS GT:AD:DP:GQ:PL 0/1:14,23:37:99:391,0,172 -chr6 52850040 rs669674 A G 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=8.43;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 52851936 rs508078 T C 1473.77 PASS AC=2;AF=1.00;AN=2;DB;DP=38;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.45;SOR=5.031;VQSLOD=7.06;culprit=FS GT:AD:DP:GQ:PL 1/1:0,38:38:99:1502,114,0 -chr6 52881235 rs11756408 C T 143.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-0.198;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.198;POSITIVE_TRAIN_SITE;QD=20.54;ReadPosRankSum=-0.922;SOR=1.609;VQSLOD=5.81;culprit=FS GT:AD:DP:GQ:PL 0/1:2,5:7:63:172,0,63 -chr6 52892683 rs222456 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52929010 rs11401639 A AT 12.93 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=6.47;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52938468 . AT A 1342.73 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-0.585;ClippingRankSum=-0.022;DP=99;FS=6.337;MLEAC=2;MLEAF=1.00;MQ=60.68;MQ0=0;MQRankSum=-0.412;POSITIVE_TRAIN_SITE;QD=13.56;ReadPosRankSum=-1.299;SOR=3.952;VQSLOD=1.47;culprit=FS GT:AD:DP:GQ:PL 1/1:2,62:64:99:1380,141,0 -chr6 52941597 rs34970749 TA T 32.71 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=16.35;SOR=0.693;VQSLOD=7.09;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 -chr6 52943841 rs35757290 TA T 559.73 PASS AC=2;AF=1.00;AN=2;DB;DP=18;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.53;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.10;SOR=5.670;VQSLOD=5.92;culprit=FS GT:AD:DP:GQ:PL 1/1:0,16:16:48:597,48,0 -chr6 52958479 rs2816350 A G 1666.77 PASS AC=2;AF=1.00;AN=2;DB;DP=45;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.49;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.21;SOR=3.816;VQSLOD=6.04;culprit=FS GT:AD:DP:GQ:PL 1/1:0,44:44:99:1695,132,0 -chr6 52962715 rs2744455 C T 1715.77 PASS AC=2;AF=1.00;AN=2;DB;DP=44;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.20;SOR=6.184;VQSLOD=5.90;culprit=FS GT:AD:DP:GQ:PL 1/1:0,44:44:99:1744,132,0 -chr6 52985368 rs6919768 T G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 52992851 rs377590473 AGAAGG A 35.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.663;ClippingRankSum=1.055;DB;DP=21;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.25;MQ0=0;MQRankSum=-2.362;QD=1.70;ReadPosRankSum=0.280;SOR=0.043;VQSLOD=3.98;culprit=FS GT:AD:DP:GQ:PL 0/1:18,3:21:73:73,0,1155 -chr6 52998788 rs2816346 G A 128.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.01;SOR=3.258;VQSLOD=7.97;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:156,12,0 -chr6 52998834 rs2816345 C T 125.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.247;ClippingRankSum=-0.163;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=-0.054;POSITIVE_TRAIN_SITE;QD=7.86;ReadPosRankSum=1.464;SOR=0.307;VQSLOD=5.43;culprit=QD GT:AD:DP:GQ:PL 0/1:10,6:16:99:154,0,317 -chr6 52998856 rs2518573 T G 225.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.191;ClippingRankSum=0.439;DB;DP=25;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.13;MQ0=0;MQRankSum=-0.322;POSITIVE_TRAIN_SITE;QD=9.03;ReadPosRankSum=-0.966;SOR=0.412;VQSLOD=4.85;culprit=FS GT:AD:DP:GQ:PL 0/1:14,10:24:99:254,0,473 -chr6 53010182 rs9367511 A G 116.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.927;ClippingRankSum=-0.533;DB;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.212;POSITIVE_TRAIN_SITE;QD=8.98;ReadPosRankSum=1.092;SOR=0.368;VQSLOD=5.93;culprit=FS GT:AD:DP:GQ:PL 0/1:8,5:13:99:145,0,291 -chr6 53010609 rs59049517 TA T 57.90 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;ClippingRankSum=0.731;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=61.53;MQ0=0;MQRankSum=-0.731;POSITIVE_TRAIN_SITE;QD=8.27;ReadPosRankSum=0.731;SOR=1.981;VQSLOD=6.42;culprit=FS GT:AD:DP:GQ:PL 0/1:1,4:5:14:95,0,14 -chr6 53061391 rs78303998 G A 114.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.017;ClippingRankSum=-0.421;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.922;QD=14.35;ReadPosRankSum=0.421;SOR=0.693;VQSLOD=4.60;culprit=FS GT:AD:DP:GQ:PL 0/1:4,4:8:99:143,0,121 -chr6 53062469 rs7772870 G A 98.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.76;SOR=1.179;VQSLOD=7.95;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:126,9,0 -chr6 53071745 rs77744774 C T 100.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.480;ClippingRankSum=-1.271;DB;DP=10;FS=6.990;MLEAC=1;MLEAF=0.500;MQ=41.67;MQ0=0;MQRankSum=-1.733;QD=10.08;ReadPosRankSum=0.000;SOR=4.407;VQSLOD=-7.559e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:2,8:10:38:129,0,38 -chr6 53072388 rs62413047 A C 120.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.447;ClippingRankSum=-0.365;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.036;POSITIVE_TRAIN_SITE;QD=12.08;ReadPosRankSum=1.133;SOR=1.329;VQSLOD=4.69;culprit=FS GT:AD:DP:GQ:PL 0/1:4,6:10:99:149,0,125 -chr6 53072441 rs11758224 A G 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.067;ClippingRankSum=-1.067;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.572;QD=3.72;ReadPosRankSum=-1.067;SOR=0.693 GT:AD:DP:GQ:PL 0/1:6,2:8:58:58,0,221 -chr6 53072501 rs11756086 T C 22.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-1.495;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.198;QD=3.26;ReadPosRankSum=-0.198;SOR=1.802 GT:AD:DP:GQ:PL 0/1:5,2:7:51:51,0,184 -chr6 53103062 rs10583094 TAC T 36.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.35;SOR=0.693;VQSLOD=8.72;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 -chr6 53119938 . G T 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 -chr6 53120011 . C T 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53173704 rs209484 C T 29.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=9.93;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:25:58,0,25 -chr6 53186203 rs209499 C T 50.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=2.303;VQSLOD=8.79;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 53210951 rs209523 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53229240 rs1346602 C T 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=7.63;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 53302223 rs11967914 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53306308 rs1401156 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53325093 rs11969450 G A 33.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=11.26;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=5.93;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:34:62,0,34 -chr6 53363487 rs10604357 GGGCT G 931.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.719;ClippingRankSum=0.942;DB;DP=65;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.90;MQ0=0;MQRankSum=-0.356;POSITIVE_TRAIN_SITE;QD=14.33;ReadPosRankSum=0.364;SOR=1.141;VQSLOD=6.29;culprit=FS GT:AD:DP:GQ:PL 0/1:37,26:63:99:969,0,1920 -chr6 53365019 rs661346 G C 4389.77 PASS AC=2;AF=1.00;AN=2;DB;DP=126;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.49;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.84;SOR=1.262;VQSLOD=6.97;culprit=QD GT:AD:DP:GQ:PL 1/1:0,125:125:99:4418,375,0 -chr6 53366008 rs12525473 C T 48.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.18;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 53366061 rs12525474 C T 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=9.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 53370107 rs661603 T C 253.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.678;ClippingRankSum=0.998;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.103;POSITIVE_TRAIN_SITE;QD=15.86;ReadPosRankSum=-0.578;SOR=0.693;VQSLOD=6.35;culprit=FS GT:AD:DP:GQ:PL 0/1:8,8:16:99:282,0,260 -chr6 53370327 rs17884019 C T 446.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.961;ClippingRankSum=-0.471;DB;DP=32;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.300;POSITIVE_TRAIN_SITE;QD=13.96;ReadPosRankSum=0.848;SOR=1.112;VQSLOD=4.70;culprit=FS GT:AD:DP:GQ:PL 0/1:16,16:32:99:475,0,461 -chr6 53372145 rs1555903 T C 760.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=5.717;ClippingRankSum=-1.830;DB;DP=57;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.171;POSITIVE_TRAIN_SITE;QD=13.35;ReadPosRankSum=0.024;SOR=0.385;VQSLOD=5.78;culprit=FS GT:AD:DP:GQ:PL 0/1:34,23:57:99:789,0,1142 -chr6 53373197 rs2235707 G C 375.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.581;ClippingRankSum=-1.193;DB;DP=25;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.250;POSITIVE_TRAIN_SITE;QD=15.03;ReadPosRankSum=0.028;SOR=0.387;VQSLOD=5.68;culprit=FS GT:AD:DP:GQ:PL 0/1:15,10:25:99:404,0,860 -chr6 53373198 rs17880319 A G 375.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.380;ClippingRankSum=-0.765;DB;DP=27;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.913;POSITIVE_TRAIN_SITE;QD=13.92;ReadPosRankSum=0.716;SOR=0.404;VQSLOD=4.81;culprit=FS GT:AD:DP:GQ:PL 0/1:16,11:27:99:404,0,860 -chr6 53373276 rs17881410 C T 1348.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.532;ClippingRankSum=-1.183;DB;DP=82;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.107;POSITIVE_TRAIN_SITE;QD=16.45;ReadPosRankSum=0.654;SOR=0.742;VQSLOD=4.98;culprit=FS GT:AD:DP:GQ:PL 0/1:40,42:82:99:1377,0,1369 -chr6 53373624 rs3830795 G GCTCCAC 706.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.129;ClippingRankSum=-1.149;DB;DP=50;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.77;MQ0=0;MQRankSum=-5.319;POSITIVE_TRAIN_SITE;QD=14.13;ReadPosRankSum=-0.966;SOR=0.399;VQSLOD=1.11;culprit=FS GT:AD:DP:GQ:PL 0/1:29,20:49:99:744,0,1894 -chr6 53378861 rs11385177 A AT 433.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.124;ClippingRankSum=-1.535;DB;DP=30;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.249;POSITIVE_TRAIN_SITE;QD=14.46;ReadPosRankSum=0.456;SOR=0.693;VQSLOD=6.60;culprit=FS GT:AD:DP:GQ:PL 0/1:15,15:30:99:471,0,469 -chr6 53379193 rs17885705 A T 3122.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.101;ClippingRankSum=-0.402;DB;DP=206;FS=0.540;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.173;POSITIVE_TRAIN_SITE;QD=15.16;ReadPosRankSum=1.720;SOR=0.781;VQSLOD=1.97;culprit=FS GT:AD:DP:GQ:PL 0/1:103,103:206:99:3151,0,3088 -chr6 53379352 rs17881444 A G 1554.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.383;ClippingRankSum=1.328;DB;DP=104;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.133;POSITIVE_TRAIN_SITE;QD=14.95;ReadPosRankSum=1.368;SOR=0.719;VQSLOD=3.93;culprit=FS GT:AD:DP:GQ:PL 0/1:55,49:104:99:1583,0,1676 -chr6 53379405 rs3736729 A C 1019.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.536;ClippingRankSum=0.059;DB;DP=50;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.059;POSITIVE_TRAIN_SITE;QD=20.40;ReadPosRankSum=-1.690;SOR=1.051;VQSLOD=4.96;culprit=FS GT:AD:DP:GQ:PL 0/1:21,29:50:99:1048,0,693 -chr6 53379499 rs17883806 G C 182.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.133;ClippingRankSum=-2.383;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.866;POSITIVE_TRAIN_SITE;QD=18.28;ReadPosRankSum=-0.741;SOR=1.085;VQSLOD=5.36;culprit=FS GT:AD:DP:GQ:PL 0/1:4,6:10:99:211,0,139 -chr6 53385934 rs17883816 T C 291.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.062;ClippingRankSum=0.766;DB;DP=15;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.237;POSITIVE_TRAIN_SITE;QD=19.45;ReadPosRankSum=1.591;SOR=1.112;VQSLOD=4.79;culprit=FS GT:AD:DP:GQ:PL 0/1:6,9:15:99:320,0,184 -chr6 53394065 rs17883125 C T 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=7.91;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 53409451 . C CCCT 53.70 PASS AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;QD=13.43;SOR=2.303;VQSLOD=6.30;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 53470507 rs9349679 G A 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 -chr6 53493640 rs6925537 T C 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.13;SOR=1.609;VQSLOD=6.84;culprit=FS GT:AD:DP:GQ:PL 1/1:0,1:1:6:83,6,0 -chr6 53493642 rs6903184 G C 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=7.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 53516876 rs6928338 T G 250.78 PASS AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=38.13;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.86;SOR=0.892;VQSLOD=6.06;culprit=FS GT:AD:DP:GQ:PL 1/1:0,9:9:27:279,27,0 -chr6 53519062 rs10948758 A G 5150.77 PASS AC=2;AF=1.00;AN=2;DB;DP=125;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.82;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.87;SOR=0.882;VQSLOD=6.17;culprit=FS GT:AD:DP:GQ:PL 1/1:0,125:125:99:5179,376,0 -chr6 53519605 rs3799260 C T 7091.77 PASS AC=2;AF=1.00;AN=2;DB;DP=190;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.76;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.12;SOR=0.693;VQSLOD=2.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,190:190:99:7120,571,0 -chr6 53519857 rs12210809 G A 4207.77 PASS AC=2;AF=1.00;AN=2;DB;DP=112;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.55;MQ0=0;POSITIVE_TRAIN_SITE;QD=36.51;SOR=1.220;VQSLOD=5.94;culprit=QD GT:AD:DP:GQ:PL 1/1:0,110:110:99:4236,331,0 -chr6 53520088 rs2038939 T C 2813.77 PASS AC=2;AF=1.00;AN=2;DB;DP=69;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.28;SOR=3.643;VQSLOD=5.42;culprit=FS GT:AD:DP:GQ:PL 1/1:0,69:69:99:2842,207,0 -chr6 53520124 rs2038940 A G 1799.77 PASS AC=2;AF=1.00;AN=2;DB;DP=46;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.50;MQ0=0;QD=29.97;SOR=6.273;VQSLOD=4.73;culprit=FS GT:AD:DP:GQ:PL 1/1:0,46:46:99:1828,138,0 -chr6 53528784 rs1326553 A G 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.43;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 53529027 rs1326554 A T 3242.77 PASS AC=2;AF=1.00;AN=2;DB;DP=87;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=37.30;SOR=4.929;VQSLOD=5.98;culprit=QD GT:AD:DP:GQ:PL 1/1:0,87:87:99:3271,262,0 -chr6 53543213 rs4541744 C T 99.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.09;SOR=1.179;VQSLOD=7.91;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:127,9,0 -chr6 53559094 rs10452610 A G 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.57;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 53586617 rs35610624 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53601883 rs7745277 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53606394 rs4457161 T C 12.07 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:23:40,0,23 -chr6 53620789 rs7763482 C T 53.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=2.303;VQSLOD=9.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 53626319 . G C 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53654033 rs3001010 C T 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.63;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 53662935 rs9382237 C T 53.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=6.56;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 53674284 rs4475321 C T 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=7.61;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 53676354 rs4715425 G A 91.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=1.179;VQSLOD=7.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:119,9,0 -chr6 53690779 rs3003489 T C 46.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.37;SOR=2.303;VQSLOD=8.83;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:74,6,0 -chr6 53691835 rs7755924 A G 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=8.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 53694407 rs6904545 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53707098 rs4286781 C T 4179.77 PASS AC=2;AF=1.00;AN=2;DB;DP=110;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.61;SOR=2.876;VQSLOD=6.95;culprit=FS GT:AD:DP:GQ:PL 1/1:0,110:110:99:4208,331,0 -chr6 53723062 rs145334901 AT A 13.89 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=6.94;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:50,6,0 -chr6 53726761 rs3935663 C T 47.79 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=15.93;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.71;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:22:76,0,22 -chr6 53726780 rs3935664 A G 90.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.09;SOR=1.179;VQSLOD=9.22;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:118,9,0 -chr6 53749074 rs4265034 G C 79.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.43;SOR=2.833;VQSLOD=8.11;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:107,9,0 -chr6 53755300 rs6458972 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53762210 rs62397108 C A 270.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.681;ClippingRankSum=-0.033;DB;DP=23;FS=4.904;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.824;POSITIVE_TRAIN_SITE;QD=11.77;ReadPosRankSum=0.890;SOR=2.165;VQSLOD=2.61;culprit=FS GT:AD:DP:GQ:PL 0/1:12,10:22:99:299,0,376 -chr6 53764829 rs71558840 T G 125.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.804;ClippingRankSum=1.304;DB;DP=26;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=39.80;MQ0=0;MQRankSum=2.136;QD=4.84;ReadPosRankSum=1.969;SOR=0.387;VQSLOD=1.71;culprit=QD GT:AD:DP:GQ:PL 0/1:15,10:25:99:154,0,298 -chr6 53778661 rs201915048 T G 38.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-5.938;ClippingRankSum=-0.459;DB;DP=84;FS=136.465;MLEAC=1;MLEAF=0.500;MQ=49.90;MQ0=0;MQRankSum=-5.277;QD=0.46;ReadPosRankSum=-6.784;SOR=6.271;VQSLOD=-4.291e+01;culprit=FS GT:AD:DP:GQ:PL 0/1:61,22:83:67:67,0,1974 -chr6 53784268 rs59246960 C CT 332.73 PASS AC=2;AF=1.00;AN=2;DB;DP=17;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.32;MQ0=0;QD=19.57;SOR=5.549;VQSLOD=4.44;culprit=FS GT:AD:DP:GQ:PL 1/1:0,15:15:45:370,45,0 -chr6 53784662 rs3777661 A G 109.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;ClippingRankSum=0.000;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.421;POSITIVE_TRAIN_SITE;QD=13.72;ReadPosRankSum=-0.421;SOR=0.693;VQSLOD=6.47;culprit=FS GT:AD:DP:GQ:PL 0/1:4,4:8:99:138,0,134 -chr6 53785276 rs2294789 C A 178.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.383;ClippingRankSum=-0.365;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.365;POSITIVE_TRAIN_SITE;QD=17.88;ReadPosRankSum=-2.072;SOR=1.085;VQSLOD=5.18;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:4,6:10:99:207,0,141 -chr6 53785759 rs201940946 G GT 45.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.550;ClippingRankSum=-0.550;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=61.34;MQ0=0;MQRankSum=-0.550;QD=5.72;ReadPosRankSum=-0.937;SOR=0.941;VQSLOD=4.79;culprit=FS GT:AD:DP:GQ:PL 0/1:3,4:7:54:83,0,54 -chr6 53787267 rs2294791 G C 221.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.074;ClippingRankSum=1.656;DB;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.935;POSITIVE_TRAIN_SITE;QD=17.06;ReadPosRankSum=0.101;SOR=0.836;VQSLOD=6.75;culprit=FS GT:AD:DP:GQ:PL 0/1:6,7:13:99:250,0,220 -chr6 53805460 rs6907354 A G 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=8.61;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 53893735 . C A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53927326 rs4715439 T C 62.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.26;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 53953083 . A G 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53973251 . G T 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 53982990 rs4521576 A C 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 53986503 rs2145754 A T 180.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.749;ClippingRankSum=1.186;DB;DP=11;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.466;POSITIVE_TRAIN_SITE;QD=16.43;ReadPosRankSum=1.932;SOR=0.859;VQSLOD=6.20;culprit=FS GT:AD:DP:GQ:PL 0/1:5,6:11:99:209,0,162 -chr6 53989526 rs4712056 G A 2189.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.153;ClippingRankSum=1.695;DB;DP=131;FS=6.808;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-1.076;POSITIVE_TRAIN_SITE;QD=16.72;ReadPosRankSum=1.657;SOR=0.326;VQSLOD=1.81;culprit=FS GT:AD:DP:GQ:PL 0/1:59,70:129:99:2218,0,1820 -chr6 54003899 rs11965480 A G 59.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=8.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 54013765 rs2145755 A G 923.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.107;ClippingRankSum=0.838;DB;DP=48;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.142;POSITIVE_TRAIN_SITE;QD=19.25;ReadPosRankSum=0.735;SOR=0.866;VQSLOD=4.39;culprit=FS GT:AD:DP:GQ:PL 0/1:22,26:48:99:952,0,728 -chr6 54025155 rs10484648 T C 760.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.724;ClippingRankSum=0.655;DB;DP=56;FS=1.455;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=-0.099;POSITIVE_TRAIN_SITE;QD=13.59;ReadPosRankSum=0.458;SOR=1.151;VQSLOD=3.37;culprit=FS GT:AD:DP:GQ:PL 0/1:30,23:53:99:789,0,990 -chr6 54030072 rs1280860 T C 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.53;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 54035531 rs2792626 T C 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=9.15;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 54046086 rs2792632 A C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54054686 rs6934690 T A 2471.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.306;ClippingRankSum=-2.348;DB;DP=167;FS=1.953;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.357;POSITIVE_TRAIN_SITE;QD=14.80;ReadPosRankSum=1.550;SOR=0.892;VQSLOD=2.86;culprit=DP GT:AD:DP:GQ:PL 0/1:79,88:167:99:2500,0,2110 -chr6 54054837 rs9296739 A G 811.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.037;ClippingRankSum=-2.468;DB;DP=45;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.876;POSITIVE_TRAIN_SITE;QD=18.04;ReadPosRankSum=-1.149;SOR=0.829;VQSLOD=5.35;culprit=FS GT:AD:DP:GQ:PL 0/1:21,24:45:99:840,0,675 -chr6 54058426 . G T 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54067088 rs67016420 AT A 245.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.880;ClippingRankSum=-0.810;DB;DP=24;FS=3.222;MLEAC=1;MLEAF=0.500;MQ=62.65;MQ0=0;MQRankSum=1.303;POSITIVE_TRAIN_SITE;QD=10.24;ReadPosRankSum=0.880;SOR=0.160;VQSLOD=2.56;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:11,10:21:99:283,0,313 -chr6 54095411 rs2275770 C G 1855.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.478;ClippingRankSum=-0.434;DB;DP=111;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=1.030;POSITIVE_TRAIN_SITE;QD=16.72;ReadPosRankSum=-1.101;SOR=0.609;VQSLOD=4.20;culprit=FS GT:AD:DP:GQ:PL 0/1:58,53:111:99:1884,0,2350 -chr6 54095423 rs816384 T C 2503.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=6.058;ClippingRankSum=-0.087;DB;DP=130;FS=7.052;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.073;POSITIVE_TRAIN_SITE;QD=19.26;ReadPosRankSum=0.105;SOR=2.758;VQSLOD=0.745;culprit=FS GT:AD:DP:GQ:PL 0/1:58,72:130:99:2532,0,2153 -chr6 54095524 rs2275769 C T 4212.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.148;ClippingRankSum=1.384;DB;DP=307;FS=2.750;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-1.330;POSITIVE_TRAIN_SITE;QD=13.72;ReadPosRankSum=0.874;SOR=0.887;VQSLOD=1.41;culprit=DP GT:AD:DP:GQ:PL 0/1:165,138:303:99:4241,0,5117 -chr6 54157748 rs6458990 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54157803 rs149997923 G GTT 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=7.05;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 54157804 rs13211037 A T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.75;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 54159866 rs7775058 C T 83.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.76;SOR=1.179;VQSLOD=7.56;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:111,9,0 -chr6 54159915 rs7740868 G T 64.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=2.833;VQSLOD=8.16;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:92,9,0 -chr6 54166206 . T C 62.74 PASS AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 54166208 . CA C 43.79 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=14.60;SOR=0.223;VQSLOD=4.47;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:19:81,0,19 -chr6 54173085 rs2297981 T A 239.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.26;SOR=4.174;VQSLOD=7.06;culprit=FS GT:AD:DP:GQ:PL 1/1:0,7:7:21:268,21,0 -chr6 54175705 rs148816365 C CTTTCTT 143 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=34.37;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.01;SOR=1.609;VQSLOD=8.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:180,12,0 -chr6 54185689 rs2297983 G T 92.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.44;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.76;SOR=2.833;VQSLOD=9.04;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:120,9,0 -chr6 54186024 rs2297986 T C 1611.77 PASS AC=2;AF=1.00;AN=2;DB;DP=43;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.67;SOR=5.235;VQSLOD=7.30;culprit=FS GT:AD:DP:GQ:PL 1/1:0,42:42:99:1640,126,0 -chr6 54186147 rs1058768 T C 3340.77 PASS AC=2;AF=1.00;AN=2;DB;DP=91;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.94;SOR=0.906;VQSLOD=4.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,91:91:99:3369,274,0 -chr6 54191363 rs9370289 G A 180.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.88;SOR=3.611;VQSLOD=5.85;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:209,15,0 -chr6 54191970 rs1848440 T A 4352.77 PASS AC=2;AF=1.00;AN=2;DB;DP=121;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.31;SOR=3.556;VQSLOD=5.90;culprit=FS GT:AD:DP:GQ:PL 1/1:0,121:121:99:4381,364,0 -chr6 54208353 rs1417387 T C 185.84 PASS AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.97;SOR=3.912;VQSLOD=6.78;culprit=FS GT:AD:DP:GQ:PL 1/1:0,6:6:18:214,18,0 -chr6 54212964 rs1876606 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54349833 rs2294725 G A 95.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.017;ClippingRankSum=0.000;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=43.31;MQ0=0;MQRankSum=0.421;POSITIVE_TRAIN_SITE;QD=11.97;ReadPosRankSum=-1.368;SOR=0.693;VQSLOD=5.69;culprit=FS GT:AD:DP:GQ:PL 0/1:4,4:8:99:124,0,121 -chr6 54350048 rs807991 G A 997.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.754;ClippingRankSum=0.019;DB;DP=73;FS=12.208;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=1.161;POSITIVE_TRAIN_SITE;QD=13.67;ReadPosRankSum=0.551;SOR=0.108;VQSLOD=1.60;culprit=FS GT:AD:DP:GQ:PL 0/1:28,38:66:99:1026,0,963 -chr6 54350422 rs565623 G A 1056.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.722;ClippingRankSum=-0.634;DB;DP=67;FS=3.327;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=0.433;POSITIVE_TRAIN_SITE;QD=15.77;ReadPosRankSum=-1.010;SOR=1.142;VQSLOD=2.92;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:32,35:67:99:1085,0,982 -chr6 54356832 rs3900305 T A 31.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=-1.231;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=6.35;ReadPosRankSum=0.358;SOR=0.368;VQSLOD=5.26;culprit=QD GT:AD:DP:GQ:PL 0/1:3,2:5:60:60,0,75 -chr6 54438922 rs10447409 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54467267 rs1951694 A G 44.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.92;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.23;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:32:73,0,32 -chr6 54477874 rs5876389 T TA 16.80 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=8.40;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:53,6,0 -chr6 54485844 rs7766941 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54489986 rs10948830 G A 2797.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.226;ClippingRankSum=-0.973;DB;DP=129;FS=4.335;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=1.300;NEGATIVE_TRAIN_SITE;QD=21.69;ReadPosRankSum=1.119;SOR=0.983;VQSLOD=-1.343e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:54,73:127:99:2826,0,2602 -chr6 54489990 rs10948831 A G 2774.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.682;ClippingRankSum=-0.704;DB;DP=125;FS=2.332;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=0.479;POSITIVE_TRAIN_SITE;QD=22.20;ReadPosRankSum=0.468;SOR=0.927;VQSLOD=0.604;culprit=DP GT:AD:DP:GQ:PL 0/1:52,71:123:99:2803,0,2545 -chr6 54490041 rs9349726 T C 2720.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=5.830;ClippingRankSum=-0.591;DB;DP=155;FS=2.034;MLEAC=1;MLEAF=0.500;MQ=58.04;MQ0=0;MQRankSum=2.054;POSITIVE_TRAIN_SITE;QD=17.55;ReadPosRankSum=0.525;SOR=0.513;VQSLOD=1.47;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:71,82:153:99:2749,0,2148 -chr6 54490338 rs10807475 T A 832.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.069;ClippingRankSum=-0.537;DB;DP=81;FS=11.744;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.204;POSITIVE_TRAIN_SITE;QD=10.28;ReadPosRankSum=0.105;SOR=0.051;VQSLOD=0.328;culprit=FS GT:AD:DP:GQ:PL 0/1:36,38:74:99:870,0,1117 -chr6 54500405 . A G 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54557514 rs1395632 G A 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:35:40,0,35 -chr6 54571089 rs6907631 T G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54635275 rs2397171 G C 38.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;ClippingRankSum=-0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.720;POSITIVE_TRAIN_SITE;QD=6.46;ReadPosRankSum=0.720;SOR=0.307;VQSLOD=5.95;culprit=QD GT:AD:DP:GQ:PL 0/1:4,2:6:67:67,0,148 -chr6 54635398 rs5876400 T TG 256.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.600;ClippingRankSum=-2.000;DB;DP=14;FS=2.363;MLEAC=1;MLEAF=0.500;MQ=51.87;MQ0=0;MQRankSum=-1.733;POSITIVE_TRAIN_SITE;QD=18.34;ReadPosRankSum=-1.467;SOR=1.288;VQSLOD=1.73;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:5,9:14:99:294,0,145 -chr6 54635417 rs4516942 G A 237.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.532;ClippingRankSum=-0.794;DB;DP=20;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.69;MQ0=0;MQRankSum=-1.172;POSITIVE_TRAIN_SITE;QD=11.89;ReadPosRankSum=-0.189;SOR=0.693;VQSLOD=4.98;culprit=FS GT:AD:DP:GQ:PL 0/1:10,10:20:99:266,0,354 -chr6 54635605 rs73742825 C G 103.03 PASS AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.07;MQ0=0;QD=17.17;SOR=1.609;VQSLOD=3.97;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:131,12,0 -chr6 54661634 rs12216186 A G 59.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.16;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 54672835 rs10807480 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54682692 . C G 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54691959 . C A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54692294 rs72957572 A G 62.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.44;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 54734941 rs7765721 C A 557.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.038;ClippingRankSum=-1.807;DB;DP=46;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=0.312;POSITIVE_TRAIN_SITE;QD=12.13;ReadPosRankSum=0.089;SOR=0.412;VQSLOD=4.55;culprit=FS GT:AD:DP:GQ:PL 0/1:27,19:46:99:586,0,962 -chr6 54735122 rs1472679 A G 2623.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.370;ClippingRankSum=-0.594;DB;DP=179;FS=1.203;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.157;POSITIVE_TRAIN_SITE;QD=14.66;ReadPosRankSum=1.205;SOR=0.798;VQSLOD=2.83;culprit=DP GT:AD:DP:GQ:PL 0/1:91,86:177:99:2652,0,2889 -chr6 54735594 rs995851 G A 418.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.928;ClippingRankSum=0.395;DB;DP=30;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.187;POSITIVE_TRAIN_SITE;QD=13.96;ReadPosRankSum=-0.686;SOR=0.576;VQSLOD=5.25;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:16,14:30:99:447,0,581 -chr6 54735606 rs995852 G A 893.77 PASS AC=2;AF=1.00;AN=2;DB;DP=23;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.18;SOR=6.358;VQSLOD=6.01;culprit=FS GT:AD:DP:GQ:PL 1/1:0,23:23:69:922,69,0 -chr6 54792553 . G A 1230.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.237;ClippingRankSum=1.275;DP=82;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=36.68;MQ0=0;MQRankSum=-1.187;QD=15.01;ReadPosRankSum=-0.624;SOR=1.402;VQSLOD=3.32;culprit=FS GT:AD:DP:GQ:PL 0/1:27,48:75:99:1259,0,685 -chr6 54807006 rs171224 T G 114.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.638;ClippingRankSum=1.368;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.421;POSITIVE_TRAIN_SITE;QD=14.35;ReadPosRankSum=-0.421;SOR=0.693;VQSLOD=6.54;culprit=FS GT:AD:DP:GQ:PL 0/1:4,4:8:99:143,0,127 -chr6 54824610 . C A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54857680 rs2134536 G A 45.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;ClippingRankSum=0.406;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.406;POSITIVE_TRAIN_SITE;QD=7.63;ReadPosRankSum=0.988;SOR=0.693;VQSLOD=5.75;culprit=QD GT:AD:DP:GQ:PL 0/1:3,3:6:73:74,0,73 -chr6 54936685 rs57552002 T TAATA 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=7.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 54938529 rs4312988 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 54998074 rs9370385 A G 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=2.303;VQSLOD=8.03;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 55003132 rs9349759 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55028053 rs200898132 CAACA C 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.60;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=6.89;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 55028113 rs6459069 C T 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.60;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=9.01;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 55040774 rs4615392 A G 50.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=0.693;VQSLOD=8.67;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 55045025 rs9370399 A C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55113411 rs3122169 C A 2001.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.942;ClippingRankSum=-1.093;DB;DP=131;FS=4.929;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.196;POSITIVE_TRAIN_SITE;QD=15.28;ReadPosRankSum=-0.937;SOR=1.302;VQSLOD=2.09;culprit=DP GT:AD:DP:GQ:PL 0/1:65,66:131:99:2030,0,2129 -chr6 55142337 rs2653349 A G 920.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.329;ClippingRankSum=-0.235;DB;DP=82;FS=3.142;MLEAC=1;MLEAF=0.500;MQ=57.13;MQ0=0;MQRankSum=0.602;POSITIVE_TRAIN_SITE;QD=11.23;ReadPosRankSum=1.940;SOR=1.110;VQSLOD=2.51;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:47,31:78:99:949,0,1545 -chr6 55142458 rs11455646 C CT 65.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.309;ClippingRankSum=-1.788;DB;DP=22;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.78;MQ0=0;MQRankSum=0.244;POSITIVE_TRAIN_SITE;QD=2.99;ReadPosRankSum=-0.380;SOR=0.446;VQSLOD=6.64;culprit=FS GT:AD:DP:GQ:PL 0/1:7,7:14:99:103,0,107 -chr6 55190480 rs12110721 G A 59.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.76;SOR=1.179;VQSLOD=7.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:87,9,0 -chr6 55196299 rs4715531 C A 87.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.09;SOR=2.833;VQSLOD=9.04;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:115,9,0 -chr6 55196587 rs12199003 C T 2169.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.778;ClippingRankSum=1.972;DB;DP=139;FS=4.029;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-0.737;POSITIVE_TRAIN_SITE;QD=15.61;ReadPosRankSum=1.585;SOR=0.438;VQSLOD=2.24;culprit=DP GT:AD:DP:GQ:PL 0/1:67,71:138:99:2198,0,1867 -chr6 55206112 rs7761953 G C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55215079 rs1032767 G A 1033.77 PASS AC=2;AF=1.00;AN=2;DB;DP=27;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.33;SOR=5.211;VQSLOD=6.59;culprit=FS GT:AD:DP:GQ:PL 1/1:0,27:27:81:1062,81,0 -chr6 55215155 rs7743512 C T 247.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.106;ClippingRankSum=1.059;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.106;POSITIVE_TRAIN_SITE;QD=15.49;ReadPosRankSum=-1.164;SOR=0.976;VQSLOD=5.41;culprit=FS GT:AD:DP:GQ:PL 0/1:7,9:16:99:276,0,215 -chr6 55216005 rs870806 G A 1207.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.265;ClippingRankSum=0.451;DB;DP=75;FS=2.105;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.005;POSITIVE_TRAIN_SITE;QD=16.10;ReadPosRankSum=0.589;SOR=0.234;VQSLOD=3.38;culprit=DP GT:AD:DP:GQ:PL 0/1:36,39:75:99:1236,0,1296 -chr6 55223501 rs41474045 T G 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=9.20;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 55223531 rs62419074 A G 95.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.763;ClippingRankSum=1.110;DB;DP=15;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.457;POSITIVE_TRAIN_SITE;QD=6.38;ReadPosRankSum=0.457;SOR=0.160;VQSLOD=4.75;culprit=QD GT:AD:DP:GQ:PL 0/1:11,4:15:99:124,0,384 -chr6 55223962 . G GTCTATCTATCTATCTA 839.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.176;ClippingRankSum=1.806;DP=80;FS=1.944;MLEAC=1;MLEAF=0.500;MQ=57.42;MQ0=0;MQRankSum=-1.121;POSITIVE_TRAIN_SITE;QD=10.50;ReadPosRankSum=-2.584;SOR=0.237;VQSLOD=1.23;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:30,22:52:99:877,0,3184 -chr6 55224107 rs9475257 A G 80.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.231;POSITIVE_TRAIN_SITE;QD=16.15;ReadPosRankSum=1.231;SOR=1.022;VQSLOD=5.30;culprit=FS GT:AD:DP:GQ:PL 0/1:2,3:5:65:109,0,65 -chr6 55227565 rs17830060 T C 48.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.57;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 55227593 rs9475263 C T 30.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.720;ClippingRankSum=0.000;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.04;MQ0=0;MQRankSum=1.380;POSITIVE_TRAIN_SITE;QD=5.13;ReadPosRankSum=-0.720;SOR=1.179;VQSLOD=5.45;culprit=QD GT:AD:DP:GQ:PL 0/1:4,2:6:59:59,0,110 -chr6 55227683 rs9475264 C G 70.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;ClippingRankSum=-0.248;DB;DP=9;FS=3.010;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.573;POSITIVE_TRAIN_SITE;QD=7.86;ReadPosRankSum=1.203;SOR=1.911;VQSLOD=1.76;culprit=QD GT:AD:DP:GQ:PL 0/1:6,3:9:99:99,0,193 -chr6 55227930 rs35444148 CA C 43.25 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=14.42;SOR=2.833;VQSLOD=8.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:80,9,0 -chr6 55258643 rs28479599 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55263789 rs9396088 C T 128.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.01;SOR=3.258;VQSLOD=7.51;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:156,12,0 -chr6 55263921 rs41271314 T C 376.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.406;ClippingRankSum=0.798;DB;DP=32;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.044;POSITIVE_TRAIN_SITE;QD=11.77;ReadPosRankSum=0.136;SOR=0.078;VQSLOD=2.13;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:20,12:32:99:405,0,694 -chr6 55264362 rs6936510 T C 1182.77 PASS AC=2;AF=1.00;AN=2;DB;DP=28;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.65;SOR=6.736;VQSLOD=6.62;culprit=FS GT:AD:DP:GQ:PL 1/1:0,28:28:84:1211,84,0 -chr6 55264461 rs6913781 C T 236.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.83;SOR=4.174;VQSLOD=6.61;culprit=FS GT:AD:DP:GQ:PL 1/1:0,7:7:21:265,21,0 -chr6 55266394 rs1546297 T A 509.77 PASS AC=2;AF=1.00;AN=2;DB;DP=13;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.23;SOR=5.283;VQSLOD=7.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,13:13:39:538,39,0 -chr6 55266625 rs9370418 T C 5961.77 PASS AC=2;AF=1.00;AN=2;DB;DP=169;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.73;SOR=1.061;VQSLOD=5.15;culprit=FS GT:AD:DP:GQ:PL 1/1:0,169:169:99:5990,508,0 -chr6 55266722 rs12529201 C T 2018.77 PASS AC=2;AF=1.00;AN=2;DB;DP=54;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.58;SOR=6.593;VQSLOD=6.37;culprit=FS GT:AD:DP:GQ:PL 1/1:0,54:54:99:2047,162,0 -chr6 55266796 rs10948913 C T 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.733;ClippingRankSum=-0.898;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.480;QD=2.38;ReadPosRankSum=1.271;SOR=0.105 GT:AD:DP:GQ:PL 0/1:8,2:10:52:52,0,252 -chr6 55275656 rs884360 A C 59.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=0.693;VQSLOD=8.35;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 55294300 rs1393326 T A 60.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=63.51;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.09;SOR=1.179;VQSLOD=7.99;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:88,9,0 -chr6 55297178 rs1032766 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55334381 rs9382495 G A 53.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=8.86;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 55357373 rs4530860 A G 71.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.76;SOR=0.693;VQSLOD=6.89;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 -chr6 55358360 rs9475318 A G 91.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=1.179;VQSLOD=8.42;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:119,9,0 -chr6 55359142 rs70986720 A AC 44.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=0.693;VQSLOD=8.16;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 55359361 rs62407080 T A 121.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.467;ClippingRankSum=0.267;DB;DP=14;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.200;POSITIVE_TRAIN_SITE;QD=8.70;ReadPosRankSum=1.067;SOR=0.307;VQSLOD=4.49;culprit=FS GT:AD:DP:GQ:PL 0/1:9,5:14:99:150,0,312 -chr6 55360086 rs4538708 A G 530.77 PASS AC=2;AF=1.00;AN=2;DB;DP=13;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.72;SOR=5.283;VQSLOD=7.04;culprit=FS GT:AD:DP:GQ:PL 1/1:0,13:13:39:559,39,0 -chr6 55361878 rs9475319 T C 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=9.03;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 55365910 rs59233169 A ACT 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=7.75;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 55368931 rs4540264 T C 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=8.52;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 55378633 rs13206666 C T 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.78;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 55381262 rs6459082 G A 5521.77 PASS AC=2;AF=1.00;AN=2;DB;DP=145;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.56;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.70;SOR=4.220;VQSLOD=6.17;culprit=FS GT:AD:DP:GQ:PL 1/1:0,145:145:99:5550,436,0 -chr6 55381574 rs9464253 T G 460.77 PASS AC=2;AF=1.00;AN=2;DB;DP=13;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.24;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.44;SOR=5.283;VQSLOD=7.38;culprit=FS GT:AD:DP:GQ:PL 1/1:0,13:13:39:489,39,0 -chr6 55381594 rs9464254 T C 300.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.19;SOR=4.407;VQSLOD=7.05;culprit=FS GT:AD:DP:GQ:PL 1/1:0,8:8:24:329,24,0 -chr6 55392955 rs7743010 C G 87.28 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.13;SOR=0.693;VQSLOD=8.45;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:9:115,9,0 -chr6 55392956 rs7743274 G A 87.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.09;SOR=1.179;VQSLOD=7.93;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:115,9,0 -chr6 55406399 rs9367638 C T 1374.77 PASS AC=2;AF=1.00;AN=2;DB;DP=36;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.41;SOR=7.223;VQSLOD=6.72;culprit=FS GT:AD:DP:GQ:PL 1/1:0,36:36:99:1403,108,0 -chr6 55425387 rs9367641 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55431875 rs9464265 C G 60.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=0.693;VQSLOD=9.15;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:88,6,0 -chr6 55471178 rs4583976 G T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55494744 . C A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55509428 rs4504466 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55519639 rs10807498 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55545792 rs34899952 C T 572.77 PASS AC=2;AF=1.00;AN=2;DB;DP=15;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.12;SOR=5.549;VQSLOD=6.57;culprit=FS GT:AD:DP:GQ:PL 1/1:0,15:15:45:601,45,0 -chr6 55625041 rs3798845 G A 44.78 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.93;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.67;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:26:73,0,26 -chr6 55714314 rs62404968 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 55730212 rs2021803 G A 169.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.969;ClippingRankSum=-0.648;DB;DP=22;FS=1.707;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.126;POSITIVE_TRAIN_SITE;QD=7.72;ReadPosRankSum=1.126;SOR=1.179;VQSLOD=2.48;culprit=QD GT:AD:DP:GQ:PL 0/1:14,8:22:99:198,0,496 -chr6 55739553 rs3734444 A G 5242.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=7.927;ClippingRankSum=0.832;DB;DP=341;FS=2.501;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=1.703;POSITIVE_TRAIN_SITE;QD=15.37;ReadPosRankSum=0.746;SOR=0.848;VQSLOD=1.42;culprit=DP GT:AD:DP:GQ:PL 0/1:176,162:338:99:5271,0,5457 -chr6 55848128 rs6911711 C T 57.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.09;SOR=1.179;VQSLOD=8.34;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:85,9,0 -chr6 55924214 rs3830813 TC T 169.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.073;ClippingRankSum=0.583;DB;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.869;POSITIVE_TRAIN_SITE;QD=13.06;ReadPosRankSum=0.779;SOR=0.693;VQSLOD=6.26;culprit=FS GT:AD:DP:GQ:PL 0/1:6,6:12:99:207,0,206 -chr6 55926067 rs181810990 T A 105.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.550;ClippingRankSum=0.550;DB;DP=7;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.550;QD=15.11;ReadPosRankSum=-0.937;SOR=2.494;VQSLOD=1.41;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:3,4:7:92:134,0,92 -chr6 55929347 rs2235735 T C 2151.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.816;ClippingRankSum=1.043;DB;DP=139;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=1.492;POSITIVE_TRAIN_SITE;QD=15.48;ReadPosRankSum=2.796;SOR=0.714;VQSLOD=2.90;culprit=FS GT:AD:DP:GQ:PL 0/1:63,75:138:99:2180,0,1872 -chr6 55929582 rs80177427 C T 195.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.989;ClippingRankSum=0.000;DB;DP=18;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.264;POSITIVE_TRAIN_SITE;QD=10.88;ReadPosRankSum=-0.996;SOR=0.368;VQSLOD=4.38;culprit=FS GT:AD:DP:GQ:PL 0/1:11,7:18:99:224,0,344 -chr6 55932035 rs138548441 A AT 3804.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.471;ClippingRankSum=-0.649;DB;DP=235;FS=5.070;MLEAC=1;MLEAF=0.500;MQ=60.13;MQ0=0;MQRankSum=-0.423;QD=16.19;ReadPosRankSum=-0.407;SOR=1.173;VQSLOD=-7.158e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:134,100:234:99:3842,0,6908 -chr6 55932036 rs62406152 C T 3813.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-5.075;ClippingRankSum=1.080;DB;DP=238;FS=5.079;MLEAC=1;MLEAF=0.500;MQ=60.22;MQ0=0;MQRankSum=1.382;QD=16.02;ReadPosRankSum=-0.395;SOR=1.179;VQSLOD=-6.900e-02;culprit=DP GT:AD:DP:GQ:PL 0/1:136,102:238:99:3842,0,6908 -chr6 55932278 rs12209529 C T 994.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.948;ClippingRankSum=0.169;DB;DP=74;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.664;POSITIVE_TRAIN_SITE;QD=13.44;ReadPosRankSum=0.071;SOR=0.463;VQSLOD=4.42;culprit=FS GT:AD:DP:GQ:PL 0/1:42,32:74:99:1023,0,1552 -chr6 55932511 rs9396171 A G 64.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=1.179;VQSLOD=8.80;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:92,9,0 -chr6 55933942 rs12189567 A G 1295.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.173;ClippingRankSum=0.118;DB;DP=97;FS=4.397;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.361;POSITIVE_TRAIN_SITE;QD=13.36;ReadPosRankSum=-0.265;SOR=0.278;VQSLOD=2.33;culprit=DP GT:AD:DP:GQ:PL 0/1:53,43:96:99:1324,0,1752 -chr6 55933987 rs12189571 A C 812.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.663;ClippingRankSum=-0.455;DB;DP=59;FS=5.997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.675;POSITIVE_TRAIN_SITE;QD=13.78;ReadPosRankSum=1.539;SOR=2.506;VQSLOD=2.27;culprit=FS GT:AD:DP:GQ:PL 0/1:33,25:58:99:841,0,1009 -chr6 55935196 rs17218309 G A 45.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.87;SOR=2.303;VQSLOD=8.20;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 -chr6 55935617 rs41271338 T C 3245.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.630;ClippingRankSum=-1.316;DB;DP=211;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.833;POSITIVE_TRAIN_SITE;QD=15.38;ReadPosRankSum=-0.759;SOR=0.734;VQSLOD=1.27;culprit=FS GT:AD:DP:GQ:PL 0/1:104,107:211:99:3274,0,3061 -chr6 55935791 rs1028390 T C 301.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.261;ClippingRankSum=1.010;DB;DP=17;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.780;POSITIVE_TRAIN_SITE;QD=17.75;ReadPosRankSum=-0.241;SOR=0.804;VQSLOD=5.58;culprit=FS GT:AD:DP:GQ:PL 0/1:8,9:17:99:330,0,267 -chr6 55938839 rs4715576 G A 104.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.774;ClippingRankSum=-0.099;DB;DP=18;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.296;POSITIVE_TRAIN_SITE;QD=5.82;ReadPosRankSum=-0.591;SOR=0.616;VQSLOD=4.82;culprit=QD GT:AD:DP:GQ:PL 0/1:13,5:18:99:133,0,453 -chr6 55942538 rs969513 G T 175.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.54;SOR=1.022;VQSLOD=6.00;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:204,15,0 -chr6 55942643 rs3065899 CAT C 36.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=63.51;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=12.24;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=2.76;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:41:74,0,41 -chr6 55942956 rs17218770 C G 1775.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.357;ClippingRankSum=0.320;DB;DP=106;FS=6.993;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=1.655;POSITIVE_TRAIN_SITE;QD=16.75;ReadPosRankSum=1.003;SOR=0.281;VQSLOD=1.69;culprit=FS GT:AD:DP:GQ:PL 0/1:50,56:106:99:1804,0,1640 -chr6 55943073 rs76049205 T C 470.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.873;ClippingRankSum=1.669;DB;DP=22;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.003;POSITIVE_TRAIN_SITE;QD=21.40;ReadPosRankSum=1.135;SOR=1.085;VQSLOD=4.22;culprit=FS GT:AD:DP:GQ:PL 0/1:9,13:22:99:499,0,281 -chr6 55943101 rs62404861 C A 242.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.366;ClippingRankSum=-0.340;DB;DP=15;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.340;POSITIVE_TRAIN_SITE;QD=16.18;ReadPosRankSum=1.324;SOR=0.818;VQSLOD=5.66;culprit=FS GT:AD:DP:GQ:PL 0/1:7,8:15:99:271,0,258 -chr6 55966027 rs12206920 C G 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.91;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 55966418 rs4379279 A G 640.77 PASS AC=2;AF=1.00;AN=2;DB;DP=16;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.42;SOR=5.670;VQSLOD=6.76;culprit=FS GT:AD:DP:GQ:PL 1/1:0,16:16:48:669,48,0 -chr6 55988619 rs41464152 T C 84.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=21.19;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=6.50;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:28:113,0,28 -chr6 55988796 rs150586735 TTA T 665.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.931;ClippingRankSum=-0.589;DB;DP=32;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.65;MQ0=0;MQRankSum=-1.804;POSITIVE_TRAIN_SITE;QD=20.80;ReadPosRankSum=0.285;SOR=0.957;VQSLOD=5.92;culprit=FS GT:AD:DP:GQ:PL 0/1:14,18:32:99:703,0,546 -chr6 55988837 . CT C 386.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.483;ClippingRankSum=-1.883;DP=57;FS=8.505;MLEAC=1;MLEAF=0.500;MQ=53.10;MQ0=0;MQRankSum=-0.083;POSITIVE_TRAIN_SITE;QD=6.78;ReadPosRankSum=0.276;SOR=2.910;VQSLOD=1.32;culprit=FS GT:AD:DP:GQ:PL 0/1:15,24:39:99:424,0,248 -chr6 55988932 rs41271844 T C 1723.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.801;ClippingRankSum=0.515;DB;DP=108;FS=2.530;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=0.871;POSITIVE_TRAIN_SITE;QD=15.96;ReadPosRankSum=0.465;SOR=0.446;VQSLOD=2.59;culprit=DP GT:AD:DP:GQ:PL 0/1:50,57:107:99:1752,0,1593 -chr6 55989320 rs12210901 T C 81.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.537;ClippingRankSum=-0.406;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.406;POSITIVE_TRAIN_SITE;QD=13.63;ReadPosRankSum=0.406;SOR=0.693;VQSLOD=6.07;culprit=FS GT:AD:DP:GQ:PL 0/1:3,3:6:97:110,0,97 -chr6 55990773 rs146607719 GTTTAC G 82.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.21;MQ0=0;MQRankSum=-0.358;POSITIVE_TRAIN_SITE;QD=16.55;ReadPosRankSum=-1.231;SOR=1.022;VQSLOD=5.99;culprit=FS GT:AD:DP:GQ:PL 0/1:2,3:5:99:120,0,131 -chr6 56006672 rs10807510 C T 2289.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=6.297;ClippingRankSum=-0.222;DB;DP=137;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.209;POSITIVE_TRAIN_SITE;QD=16.71;ReadPosRankSum=0.316;SOR=0.641;VQSLOD=3.89;culprit=FS GT:AD:DP:GQ:PL 0/1:67,70:137:99:2318,0,1931 -chr6 56021453 rs33997736 CTA C 44.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=2.303;VQSLOD=8.30;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 56021870 rs111577315 T TAAA 789.73 PASS AC=2;AF=1.00;AN=2;DB;DP=29;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.38;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.23;SOR=5.892;VQSLOD=6.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,18:18:59:827,59,0 -chr6 56021985 rs1925180 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 56021991 rs1925181 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.99;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 56022644 rs9382583 C T 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.90;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 56023811 rs994667 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56029832 rs10708181 AT A 131.80 PASS AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=14.64;SOR=3.912;VQSLOD=6.42;culprit=FS GT:AD:DP:GQ:PL 1/1:0,6:6:18:169,18,0 -chr6 56031405 rs112307837 C T 257.41 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.348;ClippingRankSum=0.696;DB;DP=11;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.393;POSITIVE_TRAIN_SITE;QD=23.40;ReadPosRankSum=0.696;SOR=3.258;VQSLOD=5.30;culprit=FS GT:AD:DP:GQ:PL 0/1:1,9:10:8:285,0,8 -chr6 56033094 rs35471617 G A 1337.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.025;ClippingRankSum=-0.876;DB;DP=117;FS=1.690;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=1.143;POSITIVE_TRAIN_SITE;QD=11.43;ReadPosRankSum=1.054;SOR=0.910;VQSLOD=2.31;culprit=DP GT:AD:DP:GQ:PL 0/1:70,47:117:99:1366,0,2112 -chr6 56037700 rs2397204 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56038131 rs9357892 A C 266.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.62;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.16;SOR=1.609;VQSLOD=6.49;culprit=FS GT:AD:DP:GQ:PL 1/1:0,7:7:21:295,21,0 -chr6 56038152 rs1925186 C G 388.77 PASS AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.39;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.093;VQSLOD=6.09;culprit=FS GT:AD:DP:GQ:PL 1/1:0,9:9:30:417,30,0 -chr6 56038178 rs9357893 G A 104.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.447;ClippingRankSum=0.633;DB;DP=11;FS=6.990;MLEAC=1;MLEAF=0.500;MQ=56.09;MQ0=0;MQRankSum=1.447;POSITIVE_TRAIN_SITE;QD=9.52;ReadPosRankSum=0.365;SOR=3.258;VQSLOD=1.97;culprit=QD GT:AD:DP:GQ:PL 0/1:6,4:10:99:133,0,206 -chr6 56038210 rs77593705 G C 155.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.470;ClippingRankSum=-1.268;DB;DP=11;FS=5.441;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=0.336;POSITIVE_TRAIN_SITE;QD=14.16;ReadPosRankSum=0.470;SOR=0.662;VQSLOD=2.59;culprit=FS GT:AD:DP:GQ:PL 0/1:5,5:10:99:184,0,147 -chr6 56044578 rs2038149 T C 10645.77 PASS AC=2;AF=1.00;AN=2;DB;DP=271;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.83;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.32;SOR=1.041;VQSLOD=2.44;culprit=FS GT:AD:DP:GQ:PL 1/1:0,271:271:99:10674,815,0 -chr6 56045043 rs2038150 C A 1313.77 PASS AC=2;AF=1.00;AN=2;DB;DP=34;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.79;SOR=7.054;VQSLOD=6.76;culprit=FS GT:AD:DP:GQ:PL 1/1:0,33:33:99:1342,99,0 -chr6 56045393 rs6933151 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56076639 rs6939465 A C 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=9.31;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 56076688 rs6939632 C T 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=8.35;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 56078396 rs6908195 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56080842 rs4126555 A G 13.72 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=6.86;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 -chr6 56090871 rs3846924 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56094789 rs1925147 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56135778 . A T 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56141614 rs141389271 G GT 509.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.917;ClippingRankSum=0.694;DB;DP=108;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=0.858;QD=4.72;ReadPosRankSum=-0.709;SOR=0.467;VQSLOD=3.58;culprit=FS GT:AD:DP:GQ:PL 0/1:34,26:60:99:547,0,668 -chr6 56149855 rs9475651 G A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.83;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 56149857 rs4715605 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.22;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 56160179 rs4432980 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56163121 rs9396195 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56184256 rs4593354 T C 59.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.25;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 56231275 rs60251615 GT G 22.73 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.36;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:59,6,0 -chr6 56241523 rs6915564 T G 134.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.51;SOR=3.258;VQSLOD=7.79;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:162,12,0 -chr6 56271872 rs10456188 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56289250 rs623582 G A 62.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 56357668 rs376190394 CA C 95.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.642;ClippingRankSum=-0.049;DB;DP=93;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=1.135;QD=1.03;ReadPosRankSum=-0.148;SOR=0.156;VQSLOD=4.06;culprit=FS GT:AD:DP:GQ:PL 0/1:52,15:67:99:133,0,976 -chr6 56365814 rs4283892 A G 5670.77 PASS AC=2;AF=1.00;AN=2;DB;DP=169;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.86;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.55;SOR=2.647;VQSLOD=4.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,169:169:99:5699,507,0 -chr6 56371698 rs9296848 A G 6846.77 PASS AC=2;AF=1.00;AN=2;DB;DP=170;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.89;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.83;SOR=7.452;VQSLOD=5.12;culprit=QD GT:AD:DP:GQ:PL 1/1:0,168:168:99:6875,506,0 -chr6 56373536 rs41271862 C T 2810.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-6.287;ClippingRankSum=-0.385;DB;DP=179;FS=1.419;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.394;POSITIVE_TRAIN_SITE;QD=15.70;ReadPosRankSum=1.719;SOR=0.556;VQSLOD=2.22;culprit=DP GT:AD:DP:GQ:PL 0/1:86,93:179:99:2839,0,2900 -chr6 56374754 rs9296849 C A 3283.77 PASS AC=2;AF=1.00;AN=2;DB;DP=86;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.38;SOR=6.689;VQSLOD=6.47;culprit=FS GT:AD:DP:GQ:PL 1/1:0,86:86:99:3312,259,0 -chr6 56380064 rs5876514 CAT C 739.73 PASS AC=2;AF=1.00;AN=2;DB;DP=18;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=62.94;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.20;SOR=5.892;VQSLOD=6.33;culprit=FS GT:AD:DP:GQ:PL 1/1:0,18:18:54:777,54,0 -chr6 56381912 rs4715626 G A 9981.77 VQSRTrancheSNP99.00to99.90 AC=2;AF=1.00;AN=2;BaseQRankSum=1.706;ClippingRankSum=-1.538;DB;DP=273;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.49;MQ0=0;MQRankSum=-1.409;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=31.78;ReadPosRankSum=1.474;SOR=2.272;VQSLOD=-5.700e-03;culprit=FS GT:AD:DP:GQ:PL 1/1:1,267:268:99:10010,795,0 -chr6 56394173 rs9357922 T C 2768.77 PASS AC=2;AF=1.00;AN=2;DB;DP=70;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=8.526;VQSLOD=7.41;culprit=FS GT:AD:DP:GQ:PL 1/1:0,70:70:99:2797,210,0 -chr6 56395051 rs6939305 C A 2021.77 PASS AC=2;AF=1.00;AN=2;DB;DP=52;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.27;SOR=7.941;VQSLOD=7.06;culprit=FS GT:AD:DP:GQ:PL 1/1:0,52:52:99:2050,157,0 -chr6 56396694 rs34224935 CT C 39.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.85;SOR=0.693;VQSLOD=7.81;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 56399731 rs7758054 A T 964.77 PASS AC=2;AF=1.00;AN=2;DB;DP=25;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.50;SOR=6.518;VQSLOD=5.73;culprit=FS GT:AD:DP:GQ:PL 1/1:0,25:25:75:993,75,0 -chr6 56401999 rs4472350 G A 91.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=2.833;VQSLOD=9.11;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:119,9,0 -chr6 56403072 . G T 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:35:40,0,35 -chr6 56410533 . G T 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56417282 rs4715630 C T 12421.77 PASS AC=2;AF=1.00;AN=2;DB;DP=331;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.31;SOR=1.081;VQSLOD=3.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,331:331:99:12450,995,0 -chr6 56417545 rs4715631 T C 10049.77 PASS AC=2;AF=1.00;AN=2;DB;DP=259;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.82;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.09;SOR=1.059;VQSLOD=4.04;culprit=FS GT:AD:DP:GQ:PL 1/1:0,259:259:99:10078,779,0 -chr6 56425284 rs2067543 A G 1201.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.751;ClippingRankSum=0.059;DB;DP=57;FS=3.927;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-0.652;POSITIVE_TRAIN_SITE;QD=21.08;ReadPosRankSum=0.296;SOR=0.220;VQSLOD=2.01;culprit=QD GT:AD:DP:GQ:PL 0/1:19,38:57:99:1230,0,587 -chr6 56425497 rs200368513 C A 36.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.37;SOR=2.303;VQSLOD=6.64;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:64,6,0 -chr6 56425900 rs1884284 G A 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=8.93;ReadPosRankSum=-0.736;SOR=1.179 GT:AD:DP:GQ:PL 0/1:1,2:3:35:55,0,35 -chr6 56425921 rs1884285 T A 80.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.920;ClippingRankSum=0.684;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.517;POSITIVE_TRAIN_SITE;QD=8.97;ReadPosRankSum=0.684;SOR=1.179;VQSLOD=4.63;culprit=FS GT:AD:DP:GQ:PL 0/1:4,5:9:99:118,0,116 -chr6 56425971 rs1884286 A G 590.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.542;ClippingRankSum=-0.814;DB;DP=30;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.374;POSITIVE_TRAIN_SITE;QD=19.69;ReadPosRankSum=-0.330;SOR=1.536;VQSLOD=5.66;culprit=FS GT:AD:DP:GQ:PL 0/1:10,20:30:99:619,0,310 -chr6 56426562 rs9357923 G A 403.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.202;ClippingRankSum=-0.527;DB;DP=23;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.837;POSITIVE_TRAIN_SITE;QD=17.56;ReadPosRankSum=-0.155;SOR=0.963;VQSLOD=5.73;culprit=FS GT:AD:DP:GQ:PL 0/1:10,13:23:99:432,0,331 -chr6 56426931 rs9367689 C T 2689.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.370;ClippingRankSum=0.043;DB;DP=192;FS=4.778;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=-0.486;POSITIVE_TRAIN_SITE;QD=14.01;ReadPosRankSum=2.114;SOR=0.409;VQSLOD=2.13;culprit=DP GT:AD:DP:GQ:PL 0/1:95,96:191:99:2718,0,3023 -chr6 56427095 rs79573569 C CTGAGTGTTGAAA 1073.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.359;ClippingRankSum=0.523;DB;DP=57;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.02;MQ0=0;MQRankSum=-4.897;POSITIVE_TRAIN_SITE;QD=18.84;ReadPosRankSum=-1.568;SOR=0.483;VQSLOD=0.980;culprit=FS GT:AD:DP:GQ:PL 0/1:32,25:57:99:1111,0,1888 -chr6 56437465 rs1014309 T C 1445.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.090;ClippingRankSum=0.209;DB;DP=89;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.79;MQ0=0;MQRankSum=1.085;POSITIVE_TRAIN_SITE;QD=16.24;ReadPosRankSum=1.427;SOR=0.648;VQSLOD=5.20;culprit=FS GT:AD:DP:GQ:PL 0/1:45,43:88:99:1474,0,1510 -chr6 56437902 rs2144405 C T 1056.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.383;ClippingRankSum=0.809;DB;DP=66;FS=1.316;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.951;POSITIVE_TRAIN_SITE;QD=16.01;ReadPosRankSum=-1.516;SOR=0.461;VQSLOD=2.55;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:31,35:66:99:1085,0,1085 -chr6 56453346 rs6919941 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56458332 . T A 301.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=2.437;ClippingRankSum=0.441;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.13;MQ0=0;MQRankSum=-3.737;QD=10.78;ReadPosRankSum=-1.927;SOR=0.460;VQSLOD=-8.078e-01;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:16,12:28:99:330,0,2663 -chr6 56458334 . G A 282.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.666;ClippingRankSum=0.476;DP=32;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.14;MQ0=0;MQRankSum=-3.134;QD=8.84;ReadPosRankSum=-0.992;SOR=0.260;VQSLOD=0.189;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:21,11:32:99:311,0,3242 -chr6 56458337 . G A 260.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.343;ClippingRankSum=-0.083;DP=38;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.95;MQ0=0;MQRankSum=-3.199;QD=6.86;ReadPosRankSum=-0.878;SOR=0.134;VQSLOD=-4.171e-01;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:28,10:38:99:289,0,3630 -chr6 56458338 . T A 215.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=4.133;ClippingRankSum=-0.659;DP=39;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.08;MQ0=0;MQRankSum=-3.522;NEGATIVE_TRAIN_SITE;QD=5.53;ReadPosRankSum=-2.300;SOR=0.126;VQSLOD=-2.429e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:29,10:39:99:244,0,3725 -chr6 56458339 . AGGCT A 206.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.653;ClippingRankSum=-1.136;DP=43;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.56;MQ0=0;MQRankSum=-3.349;QD=4.81;ReadPosRankSum=-3.027;SOR=0.100;VQSLOD=-5.999e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:33,10:43:99:244,0,3725 -chr6 56462840 rs9370541 G A 2994.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.431;ClippingRankSum=-1.553;DB;DP=213;FS=6.435;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=0.686;POSITIVE_TRAIN_SITE;QD=14.06;ReadPosRankSum=0.540;SOR=1.216;VQSLOD=2.10;culprit=DP GT:AD:DP:GQ:PL 0/1:118,95:213:99:3023,0,3656 -chr6 56463410 rs4712138 T C 5519.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-7.361;ClippingRankSum=-0.682;DB;DP=398;FS=13.317;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=0.637;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=13.87;ReadPosRankSum=2.315;SOR=0.352;VQSLOD=-4.795e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:208,189:397:99:5548,0,6660 -chr6 56466999 rs9382653 T G 75.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.21;MQ0=0;MQRankSum=0.358;POSITIVE_TRAIN_SITE;QD=15.15;ReadPosRankSum=1.231;SOR=1.022;VQSLOD=6.62;culprit=FS GT:AD:DP:GQ:PL 0/1:2,3:5:63:104,0,63 -chr6 56467586 rs11751914 G A 530.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.043;ClippingRankSum=1.304;DB;DP=35;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.403;POSITIVE_TRAIN_SITE;QD=15.16;ReadPosRankSum=1.601;SOR=0.641;VQSLOD=5.46;culprit=FS GT:AD:DP:GQ:PL 0/1:18,17:35:99:559,0,665 -chr6 56468238 rs9370543 G A 3348.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=8.795;ClippingRankSum=0.055;DB;DP=200;FS=1.921;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.619;POSITIVE_TRAIN_SITE;QD=16.74;ReadPosRankSum=2.983;SOR=0.871;VQSLOD=2.18;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:102,97:199:99:3377,0,3183 -chr6 56468537 rs9382656 T C 5633.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=8.003;ClippingRankSum=-2.016;DB;DP=287;FS=2.022;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.379;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=19.63;ReadPosRankSum=-1.151;SOR=0.827;VQSLOD=0.525;culprit=DP GT:AD:DP:GQ:PL 0/1:124,162:286:99:5662,0,3728 -chr6 56470551 rs13194995 T A 4264.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.507;ClippingRankSum=-0.154;DB;DP=311;FS=0.415;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-0.365;POSITIVE_TRAIN_SITE;QD=13.71;ReadPosRankSum=0.256;SOR=0.662;VQSLOD=1.73;culprit=FS GT:AD:DP:GQ:PL 0/1:169,141:310:99:4293,0,5525 -chr6 56470690 rs13209548 G A 4581.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.221;ClippingRankSum=0.043;DB;DP=298;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-1.592;POSITIVE_TRAIN_SITE;QD=15.38;ReadPosRankSum=1.757;SOR=0.668;VQSLOD=1.27;culprit=FS GT:AD:DP:GQ:PL 0/1:151,147:298:99:4610,0,4504 -chr6 56471402 rs9382658 G A 5089.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.363;ClippingRankSum=0.422;DB;DP=342;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.581;POSITIVE_TRAIN_SITE;QD=14.88;ReadPosRankSum=0.721;SOR=0.676;VQSLOD=1.79;culprit=FS GT:AD:DP:GQ:PL 0/1:182,158:340:99:5118,0,6087 -chr6 56471995 rs16888055 C T 2905.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-6.315;ClippingRankSum=0.444;DB;DP=194;FS=5.194;MLEAC=1;MLEAF=0.500;MQ=59.69;MQ0=0;MQRankSum=0.379;POSITIVE_TRAIN_SITE;QD=14.98;ReadPosRankSum=1.462;SOR=1.052;VQSLOD=2.30;culprit=DP GT:AD:DP:GQ:PL 0/1:97,95:192:99:2934,0,3313 -chr6 56476023 rs9370544 G A 43.78 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.59;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.14;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:27:72,0,27 -chr6 56476182 rs10643818 T TAAGTA 257.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.783;ClippingRankSum=0.790;DB;DP=31;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.17;MQ0=0;MQRankSum=-1.828;POSITIVE_TRAIN_SITE;QD=8.31;ReadPosRankSum=-0.384;SOR=0.132;VQSLOD=5.82;culprit=FS GT:AD:DP:GQ:PL 0/1:23,8:31:99:295,0,1187 -chr6 56476262 rs7747060 T C 1532.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.526;ClippingRankSum=-0.045;DB;DP=116;FS=1.204;MLEAC=1;MLEAF=0.500;MQ=58.89;MQ0=0;MQRankSum=-0.777;POSITIVE_TRAIN_SITE;QD=13.21;ReadPosRankSum=-0.453;SOR=0.898;VQSLOD=2.87;culprit=DP GT:AD:DP:GQ:PL 0/1:67,49:116:99:1561,0,2190 -chr6 56476456 rs9396226 T A 997.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.112;ClippingRankSum=0.345;DB;DP=87;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=0.224;POSITIVE_TRAIN_SITE;QD=11.47;ReadPosRankSum=0.466;SOR=0.980;VQSLOD=4.80;culprit=FS GT:AD:DP:GQ:PL 0/1:34,44:78:99:1035,0,1041 -chr6 56482704 rs9396228 A C 747.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=5.823;ClippingRankSum=-0.173;DB;DP=72;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.209;POSITIVE_TRAIN_SITE;QD=10.39;ReadPosRankSum=2.168;SOR=0.735;VQSLOD=4.91;culprit=FS GT:AD:DP:GQ:PL 0/1:48,24:72:99:776,0,1600 -chr6 56482801 rs6459166 C G 2911.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.925;ClippingRankSum=0.679;DB;DP=217;FS=5.006;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=0.577;POSITIVE_TRAIN_SITE;QD=13.42;ReadPosRankSum=1.457;SOR=1.052;VQSLOD=2.17;culprit=DP GT:AD:DP:GQ:PL 0/1:119,98:217:99:2940,0,3555 -chr6 56484758 rs2230862 C T 1769.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-6.905;ClippingRankSum=1.335;DB;DP=147;FS=6.412;MLEAC=1;MLEAF=0.500;MQ=56.34;MQ0=0;MQRankSum=1.822;POSITIVE_TRAIN_SITE;QD=12.04;ReadPosRankSum=0.721;SOR=0.357;VQSLOD=1.58;culprit=FS GT:AD:DP:GQ:PL 0/1:86,61:147:99:1798,0,2992 -chr6 56496649 rs10456737 A C 1638.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.101;ClippingRankSum=-1.291;DB;DP=80;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-0.160;POSITIVE_TRAIN_SITE;QD=20.48;ReadPosRankSum=0.671;SOR=0.763;VQSLOD=5.14;culprit=FS GT:AD:DP:GQ:PL 0/1:29,51:80:99:1667,0,816 -chr6 56507135 rs1024195 T C 1136.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.677;ClippingRankSum=0.952;DB;DP=56;FS=1.927;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.207;POSITIVE_TRAIN_SITE;QD=20.30;ReadPosRankSum=-0.108;SOR=1.511;VQSLOD=2.71;culprit=QD GT:AD:DP:GQ:PL 0/1:24,32:56:99:1165,0,749 -chr6 56701620 . G T 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=36.50;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56736574 . TA T 49.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.817;ClippingRankSum=1.184;DP=26;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=0.531;QD=1.91;ReadPosRankSum=1.312;SOR=0.602;VQSLOD=4.48;culprit=FS GT:AD:DP:GQ:PL 0/1:10,9:19:87:87,0,131 -chr6 56818706 rs986245 T C 816.77 PASS AC=2;AF=1.00;AN=2;DB;DP=24;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.03;SOR=2.925;VQSLOD=6.74;culprit=FS GT:AD:DP:GQ:PL 1/1:0,24:24:72:845,72,0 -chr6 56827628 rs9349841 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56846334 rs9396247 A G 342.78 PASS AC=2;AF=1.00;AN=2;DB;DP=9;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.76;SOR=4.615;VQSLOD=6.28;culprit=FS GT:AD:DP:GQ:PL 1/1:0,9:9:27:371,27,0 -chr6 56873069 rs6925819 T C 1050.77 PASS AC=2;AF=1.00;AN=2;DB;DP=30;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.45;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.57;SOR=3.912;VQSLOD=6.47;culprit=FS GT:AD:DP:GQ:PL 1/1:0,30:30:90:1079,90,0 -chr6 56893978 rs58747062 TC T 28.71 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=14.35;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:65,6,0 -chr6 56894940 rs34180205 CG C 106 PASS AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.20;SOR=3.258;VQSLOD=5.74;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:143,12,0 -chr6 56900699 rs3996934 C T 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=8.71;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 56917538 rs6926980 G A 2244.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.357;ClippingRankSum=0.056;DB;DP=147;FS=7.253;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.138;POSITIVE_TRAIN_SITE;QD=15.27;ReadPosRankSum=2.288;SOR=0.714;VQSLOD=2.13;culprit=FS GT:AD:DP:GQ:PL 0/1:74,73:147:99:2273,0,2345 -chr6 56919443 rs61740375 A G 752.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.392;ClippingRankSum=-0.128;DB;DP=52;FS=10.283;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.769;POSITIVE_TRAIN_SITE;QD=14.48;ReadPosRankSum=1.044;SOR=0.065;VQSLOD=1.36;culprit=FS GT:AD:DP:GQ:PL 0/1:27,25:52:99:781,0,941 -chr6 56963708 rs9367711 T G 789.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.396;ClippingRankSum=-0.682;DB;DP=55;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.513;POSITIVE_TRAIN_SITE;QD=14.36;ReadPosRankSum=0.295;SOR=0.729;VQSLOD=5.51;culprit=FS GT:AD:DP:GQ:PL 0/1:27,28:55:99:818,0,939 -chr6 56994594 rs7758913 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 56998023 rs3757296 A G 2007.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.613;ClippingRankSum=-0.822;DB;DP=133;FS=2.401;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=-0.518;POSITIVE_TRAIN_SITE;QD=15.10;ReadPosRankSum=-1.605;SOR=0.503;VQSLOD=2.33;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:64,67:131:99:2036,0,2080 -chr6 57006391 rs2273919 C T 310.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.573;ClippingRankSum=-0.380;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=1.356;POSITIVE_TRAIN_SITE;QD=19.42;ReadPosRankSum=2.007;SOR=1.244;VQSLOD=5.45;culprit=FS GT:AD:DP:GQ:PL 0/1:6,10:16:99:339,0,197 -chr6 57006933 rs2273921 T C 1686.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.719;ClippingRankSum=0.791;DB;DP=136;FS=8.160;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.554;POSITIVE_TRAIN_SITE;QD=12.40;ReadPosRankSum=0.949;SOR=1.463;VQSLOD=2.01;culprit=FS GT:AD:DP:GQ:PL 0/1:76,60:136:99:1715,0,2402 -chr6 57012930 rs3734738 C T 2118.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.567;ClippingRankSum=-0.086;DB;DP=161;FS=1.455;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.460;POSITIVE_TRAIN_SITE;QD=13.16;ReadPosRankSum=-1.077;SOR=0.558;VQSLOD=2.37;culprit=DP GT:AD:DP:GQ:PL 0/1:87,74:161:99:2147,0,2812 -chr6 57048458 rs9885757 C T 476.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.695;ClippingRankSum=-0.057;DB;DP=32;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=0.057;POSITIVE_TRAIN_SITE;QD=14.90;ReadPosRankSum=0.019;SOR=0.693;VQSLOD=5.92;culprit=FS GT:AD:DP:GQ:PL 0/1:16,16:32:99:505,0,556 -chr6 57055354 rs1040461 C T 2987.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.147;ClippingRankSum=-2.243;DB;DP=178;FS=1.900;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.750;POSITIVE_TRAIN_SITE;QD=16.79;ReadPosRankSum=0.605;SOR=0.855;VQSLOD=2.11;culprit=DP GT:AD:DP:GQ:PL 0/1:81,97:178:99:3016,0,2448 -chr6 57059820 rs9357940 T G 252.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.739;ClippingRankSum=0.627;DB;DP=14;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.739;POSITIVE_TRAIN_SITE;QD=18.05;ReadPosRankSum=0.715;SOR=0.976;VQSLOD=6.00;culprit=FS GT:AD:DP:GQ:PL 0/1:6,8:14:99:281,0,187 -chr6 57074911 rs9357941 G A 404.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.359;ClippingRankSum=-0.103;DB;DP=26;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.462;POSITIVE_TRAIN_SITE;QD=15.57;ReadPosRankSum=-1.538;SOR=0.693;VQSLOD=5.41;culprit=FS GT:AD:DP:GQ:PL 0/1:13,13:26:99:433,0,497 -chr6 57097549 rs223304 T C 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=2.303;VQSLOD=9.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 57106426 rs223289 T G 50.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.37;SOR=2.303;VQSLOD=8.94;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 57163494 rs7770252 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57182297 rs1019210 C T 63.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=6.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 57183869 . A T 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:34:40,0,34 -chr6 57188889 rs79594432 A T 460.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.171;ClippingRankSum=0.415;DB;DP=27;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.756;POSITIVE_TRAIN_SITE;QD=17.07;ReadPosRankSum=-0.512;SOR=0.922;VQSLOD=5.20;culprit=FS GT:AD:DP:GQ:PL 0/1:12,15:27:99:489,0,381 -chr6 57191021 rs11381745 A AG 1131.73 PASS AC=2;AF=1.00;AN=2;DB;DP=39;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.10;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.02;SOR=7.054;VQSLOD=6.03;culprit=FS GT:AD:DP:GQ:PL 1/1:0,33:33:99:1169,99,0 -chr6 57209749 rs9475860 C T 48.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.37;SOR=2.303;VQSLOD=6.73;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 57209802 rs1024706 T C 63.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.09;SOR=1.179;VQSLOD=7.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 57209865 rs5876534 GA G 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=7.46;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57209889 rs1024705 G T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.52;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57213782 rs7772897 A G 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57213785 rs7755104 T C 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57226182 rs17705499 C T 51.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.727;POSITIVE_TRAIN_SITE;QD=12.94;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=6.47;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:29:80,0,29 -chr6 57228571 rs12193422 G A 48.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=16.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.15;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:29:77,0,29 -chr6 57228598 rs6911124 A G 51.79 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.727;QD=12.95;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.09;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:23:80,0,23 -chr6 57228685 rs6911177 A G 123.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.380;ClippingRankSum=-0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.720;QD=20.63;ReadPosRankSum=-0.720;SOR=0.693;VQSLOD=4.71;culprit=FS GT:AD:DP:GQ:PL 0/1:2,4:6:99:152,0,126 -chr6 57228704 rs6934266 T G 46.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.358;QD=9.35;ReadPosRankSum=0.358;SOR=0.368;VQSLOD=4.40;culprit=FS GT:AD:DP:GQ:PL 0/1:3,2:5:75:75,0,154 -chr6 57228809 rs6911507 A C 50.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=16.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.92;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:32:79,0,32 -chr6 57231331 rs2079934 G T 32.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=63.51;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=10.92;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=6.36;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:32:61,0,32 -chr6 57231352 rs2397239 T C 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57231354 rs2397240 A G 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57232345 rs12200857 G A 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:28:40,0,28 -chr6 57232902 rs62417969 T G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57234078 rs9464454 A C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57243144 rs12201524 G A 49.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.026;QD=12.44;ReadPosRankSum=0.000;SOR=0.105;VQSLOD=4.21;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,154 -chr6 57243154 rs12201527 G A 49.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;QD=12.44;ReadPosRankSum=0.000;SOR=0.105;VQSLOD=4.91;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,154 -chr6 57244492 rs7759919 T C 24.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.572;ClippingRankSum=-1.067;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.572;QD=3.10;ReadPosRankSum=-1.067;SOR=0.169 GT:AD:DP:GQ:PL 0/1:6,2:8:53:53,0,209 -chr6 57244509 rs5011405 T G 34.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.589;ClippingRankSum=1.589;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.067;POSITIVE_TRAIN_SITE;QD=4.35;ReadPosRankSum=-0.572;SOR=0.169;VQSLOD=5.46;culprit=QD GT:AD:DP:GQ:PL 0/1:6,2:8:63:63,0,213 -chr6 57244672 rs5011404 G A 2178.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.306;ClippingRankSum=2.205;DB;DP=136;FS=2.003;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-0.847;POSITIVE_TRAIN_SITE;QD=16.02;ReadPosRankSum=0.446;SOR=1.017;VQSLOD=2.92;culprit=DP GT:AD:DP:GQ:PL 0/1:66,70:136:99:2207,0,2213 -chr6 57244780 rs5011403 G A 3287.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.453;ClippingRankSum=0.408;DB;DP=235;FS=0.510;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=0.808;QD=13.99;ReadPosRankSum=0.963;SOR=0.634;VQSLOD=0.424;culprit=FS GT:AD:DP:GQ:PL 0/1:123,112:235:99:3316,0,3653 -chr6 57244830 rs5011402 T A 2187.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.318;ClippingRankSum=1.365;DB;DP=134;FS=4.341;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-1.290;QD=16.33;ReadPosRankSum=0.292;SOR=0.162;VQSLOD=0.141;culprit=DP GT:AD:DP:GQ:PL 0/1:64,70:134:99:2216,0,2120 -chr6 57244893 rs5011401 T C 609.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.502;ClippingRankSum=-0.431;DB;DP=34;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.260;POSITIVE_TRAIN_SITE;QD=17.93;ReadPosRankSum=2.018;SOR=0.811;VQSLOD=4.32;culprit=FS GT:AD:DP:GQ:PL 0/1:16,18:34:99:638,0,509 -chr6 57244979 rs5011400 G A 91.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=1.231;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.96;MQ0=0;MQRankSum=-1.231;QD=18.35;ReadPosRankSum=0.358;SOR=1.022;VQSLOD=4.54;culprit=FS GT:AD:DP:GQ:PL 0/1:2,3:5:99:120,0,137 -chr6 57244982 rs5011399 C T 91.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=-0.358;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.96;MQ0=0;MQRankSum=-1.231;QD=18.35;ReadPosRankSum=0.358;SOR=1.022;VQSLOD=4.34;culprit=FS GT:AD:DP:GQ:PL 0/1:2,3:5:99:120,0,137 -chr6 57246581 rs62415468 T A 183.85 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.742;ClippingRankSum=-0.742;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.62;MQ0=0;MQRankSum=-0.742;QD=26.26;ReadPosRankSum=-0.742;SOR=2.584;VQSLOD=3.61;culprit=FS GT:AD:DP:GQ:PL 0/1:1,6:7:17:212,0,17 -chr6 57246614 rs62415469 T C 379.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.371;ClippingRankSum=-2.285;DB;DP=15;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.718;QD=25.32;ReadPosRankSum=-1.371;SOR=1.911;VQSLOD=3.76;culprit=FS GT:AD:DP:GQ:PL 0/1:4,11:15:99:408,0,118 -chr6 57246638 rs6913328 C T 668.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.214;ClippingRankSum=-1.226;DB;DP=32;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.603;QD=20.90;ReadPosRankSum=1.654;SOR=1.284;VQSLOD=3.38;culprit=FS GT:AD:DP:GQ:PL 0/1:12,20:32:99:697,0,376 -chr6 57246708 rs6913779 G T 1443.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-8.155;ClippingRankSum=0.128;DB;DP=141;FS=4.590;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=-1.089;QD=10.24;ReadPosRankSum=-0.829;SOR=0.067;VQSLOD=-7.831e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:92,49:141:99:1472,0,3506 -chr6 57246773 rs113849959 T TAGG 4992.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.588;ClippingRankSum=0.124;DB;DP=309;FS=5.829;MLEAC=1;MLEAF=0.500;MQ=57.08;MQ0=0;MQRankSum=-3.483;NEGATIVE_TRAIN_SITE;QD=16.16;ReadPosRankSum=1.260;SOR=1.145;VQSLOD=-2.405e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:174,127:301:99:5030,0,7083 -chr6 57246785 rs62415470 A C 5492.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=8.898;ClippingRankSum=-0.346;DB;DP=349;FS=1.043;MLEAC=1;MLEAF=0.500;MQ=57.28;MQ0=0;MQRankSum=-1.730;QD=15.74;ReadPosRankSum=1.758;SOR=0.781;VQSLOD=-7.042e-01;culprit=DP GT:AD:DP:GQ:PL 0/1:201,148:349:99:5521,0,7683 -chr6 57246815 rs6936571 T C 5593.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=6.746;ClippingRankSum=-1.594;DB;DP=416;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-1.167;NEGATIVE_TRAIN_SITE;QD=13.45;ReadPosRankSum=-1.267;SOR=0.707;VQSLOD=-1.509e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:229,187:416:99:5622,0,7181 -chr6 57246878 rs61753604 T C 1938.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.885;ClippingRankSum=1.162;DB;DP=444;FS=0.650;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=-1.757;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=4.37;ReadPosRankSum=0.012;SOR=0.802;VQSLOD=-1.920e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:350,94:444:99:1967,0,13279 -chr6 57246884 rs6913546 A G 7065.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=3.408;ClippingRankSum=-0.389;DB;DP=440;FS=0.524;MLEAC=1;MLEAF=0.500;MQ=58.70;MQ0=0;MQRankSum=-2.305;NEGATIVE_TRAIN_SITE;QD=16.06;ReadPosRankSum=-1.094;SOR=0.630;VQSLOD=-2.286e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:227,212:439:99:7094,0,7015 -chr6 57246969 rs4256440 G A 4783.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-7.872;ClippingRankSum=0.620;DB;DP=347;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=0;MQRankSum=-0.808;QD=13.79;ReadPosRankSum=-0.427;SOR=0.712;VQSLOD=-4.860e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:182,163:345:99:4812,0,6048 -chr6 57246982 rs4585567 G T 4000.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-7.751;ClippingRankSum=0.330;DB;DP=315;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-0.546;QD=12.70;ReadPosRankSum=-0.935;SOR=0.712;VQSLOD=-5.530e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:174,139:313:99:4029,0,5824 -chr6 57247022 rs4382263 C T 3135.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.094;ClippingRankSum=-0.825;DB;DP=206;FS=9.797;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=0.277;QD=15.22;ReadPosRankSum=0.532;SOR=1.811;VQSLOD=-7.670e-02;culprit=FS GT:AD:DP:GQ:PL 0/1:108,98:206:99:3164,0,3645 -chr6 57247093 rs4499918 A T 892.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.606;ClippingRankSum=0.186;DB;DP=63;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.52;MQ0=0;MQRankSum=0.131;QD=14.17;ReadPosRankSum=-0.517;SOR=0.551;VQSLOD=2.59;culprit=FS GT:AD:DP:GQ:PL 0/1:34,29:63:99:921,0,1186 -chr6 57247108 rs4507595 G A 668.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.825;ClippingRankSum=0.298;DB;DP=53;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=-0.262;QD=12.62;ReadPosRankSum=0.406;SOR=0.416;VQSLOD=3.79;culprit=FS GT:AD:DP:GQ:PL 0/1:31,22:53:99:697,0,1110 -chr6 57247121 rs4310040 T C 577.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.370;ClippingRankSum=-1.834;DB;DP=43;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=-0.849;QD=13.44;ReadPosRankSum=-0.382;SOR=0.428;VQSLOD=3.58;culprit=FS GT:AD:DP:GQ:PL 0/1:25,18:43:99:606,0,856 -chr6 57259789 rs149275162 C A 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.23;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57259808 rs117189504 A T 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57259820 rs114240725 C T 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57260463 rs9475913 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57262992 rs2894847 A G 11.83 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.83;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0 -chr6 57263008 rs72871660 G C 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.87;SOR=2.303;VQSLOD=7.01;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 57284914 . G T 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57296209 rs78775831 G A 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=9.30;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57296216 rs80242777 C A 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=9.30;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57296249 rs72873542 C G 16.63 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=8.31;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:43,3,0 -chr6 57303056 rs62401712 T C 40.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=13.59;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=4.28;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:29:69,0,29 -chr6 57303102 rs62401713 A G 15.43 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=5.14;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:1:41,0,1 -chr6 57307716 rs60930046 T C 40.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=20.37;SOR=2.303;VQSLOD=6.63;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 57307784 rs60600423 C G 73.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=24.43;SOR=1.179;VQSLOD=5.30;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:101,9,0 -chr6 57309839 rs5003056 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57310132 rs73750278 C G 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57310138 rs73750279 C A 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57310284 rs9464491 A G 40.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=5.91;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 57310326 rs73750281 T G 52.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.47;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 -chr6 57310334 rs73750282 T C 52.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.59;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 -chr6 57315082 rs12204748 G A 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.37;SOR=0.693;VQSLOD=7.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 57325633 rs4715697 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57326248 rs2145339 A G 48.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.37;SOR=0.693;VQSLOD=7.07;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 57326568 rs9464502 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57330320 rs9382742 T C 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=9.34;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 57336157 rs9476010 G A 30.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.380;ClippingRankSum=0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.380;QD=5.13;ReadPosRankSum=0.000;SOR=0.693;VQSLOD=3.01;culprit=QD GT:AD:DP:GQ:PL 0/1:4,2:6:59:59,0,154 -chr6 57336243 rs9476012 G A 39.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.026;QD=9.94;ReadPosRankSum=0.000;SOR=0.105;VQSLOD=3.79;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:68:68,0,78 -chr6 57336279 rs9476013 C G 49.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.000;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;QD=12.44;ReadPosRankSum=0.000;SOR=0.105;VQSLOD=4.91;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,78 -chr6 57336284 rs9476014 A G 49.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.000;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;QD=12.44;ReadPosRankSum=1.026;SOR=0.105;VQSLOD=4.33;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,78 -chr6 57336340 rs1570072 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57342040 rs13219968 T C 63.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.09;SOR=1.179;VQSLOD=7.17;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 57345089 rs5024768 G C 40.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=6.41;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 57347208 . T TG 21.73 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.87;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:58,6,0 -chr6 57347800 rs34877937 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.09;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57347818 rs35142105 T G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.18;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57348150 rs34523439 G A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.16;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57348155 rs35239416 A T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.42;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57348440 rs34411188 A G 50.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=0.736;QD=16.92;ReadPosRankSum=-0.736;SOR=2.225;VQSLOD=1.11;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:1,2:3:28:79,0,28 -chr6 57348501 rs35975405 T C 71.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.34;culprit=DP GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 -chr6 57348518 rs71221642 A G 71.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.40;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 -chr6 57348534 rs34153534 G A 107.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.69;SOR=1.179;VQSLOD=7.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 57348538 rs34509185 T G 107.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=35.33;SOR=1.179;VQSLOD=6.95;culprit=QD GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 57349040 rs9476023 T C 93.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.09;SOR=1.179;VQSLOD=7.46;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:121,9,0 -chr6 57349257 rs9476024 C T 16.63 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=16.63;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:43,3,0 -chr6 57349280 rs12198778 A G 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.37;SOR=2.303;VQSLOD=7.09;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 57349405 rs9476025 A G 17.61 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=17.61;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:44,3,0 -chr6 57349426 rs9476026 C T 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.34;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57349572 rs6929331 A G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=9.11;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57349576 rs4715714 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=9.46;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57350134 rs9367752 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57353249 rs4715715 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57355968 rs35947597 T A 102.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.09;SOR=1.179;VQSLOD=7.02;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:130,9,0 -chr6 57355975 . C A 102.28 PASS AC=2;AF=1.00;AN=2;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.09;SOR=1.179;VQSLOD=5.89;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:130,9,0 -chr6 57355995 rs36115431 G A 102.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.09;SOR=1.179;VQSLOD=6.91;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:130,9,0 -chr6 57356611 rs9476033 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57358196 rs36181256 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57358870 rs4991170 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57358888 rs5876577 T TC 37.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.85;SOR=0.693;VQSLOD=7.35;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:74,6,0 -chr6 57362013 rs62399733 T C 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:31:40,0,31 -chr6 57362029 rs73752496 A G 52.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.73;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:74:81,0,74 -chr6 57362030 rs72877164 C T 52.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.56;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:74:81,0,74 -chr6 57362057 rs12526351 G A 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:36:40,0,36 -chr6 57364996 rs73755520 C T 32.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-1.026;QD=8.19;ReadPosRankSum=0.000;SOR=0.105;VQSLOD=3.31;culprit=QD GT:AD:DP:GQ:PL 0/1:2,2:4:61:61,0,76 -chr6 57365151 rs5025370 T C 47.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=15.92;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=5.00;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:35:76,0,35 -chr6 57366534 rs4715718 G T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.68;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57366536 rs4715719 A T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.49;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57368219 rs62400883 G A 36.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=-0.736;QD=12.26;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.12;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:30:65,0,30 -chr6 57369510 rs62400894 A G 40.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=6.89;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 57371913 rs59066164 G A 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57371916 rs75944038 G A 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57371926 rs10949092 A T 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57371931 rs74978393 G A 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57371939 rs10949093 G A 53.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=26.87;SOR=0.693;VQSLOD=7.42;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 57371962 rs10949094 T A 48.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=24.37;SOR=0.693;VQSLOD=6.34;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 57372104 rs2024986 T C 162.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.512;ClippingRankSum=0.514;DB;DP=25;FS=5.528;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.091;QD=6.51;ReadPosRankSum=0.212;SOR=0.033;VQSLOD=0.457;culprit=QD GT:AD:DP:GQ:PL 0/1:18,7:25:99:191,0,669 -chr6 57372116 rs9382768 T C 752.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.259;ClippingRankSum=0.589;DB;DP=29;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.589;QD=25.96;ReadPosRankSum=-0.778;SOR=1.688;VQSLOD=2.67;culprit=FS GT:AD:DP:GQ:PL 0/1:9,20:29:99:781,0,276 -chr6 57372126 rs9396314 C G 253.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.170;ClippingRankSum=-1.868;DB;DP=35;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.510;POSITIVE_TRAIN_SITE;QD=7.25;ReadPosRankSum=0.698;SOR=0.129;VQSLOD=4.41;culprit=QD GT:AD:DP:GQ:PL 0/1:26,9:35:99:282,0,1018 -chr6 57372199 rs9382769 T C 3132.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=8.094;ClippingRankSum=0.441;DB;DP=131;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.586;QD=23.91;ReadPosRankSum=-0.007;SOR=1.470;VQSLOD=1.39;culprit=FS GT:AD:DP:GQ:PL 0/1:46,85:131:99:3161,0,1398 -chr6 57372361 rs9382770 C A 10336.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-5.385;ClippingRankSum=-0.913;DB;DP=437;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=1.326;NEGATIVE_TRAIN_SITE;QD=23.65;ReadPosRankSum=0.567;SOR=0.720;VQSLOD=-2.151e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:149,287:436:99:10365,0,4146 -chr6 57372365 rs9396315 A G 3727.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.398;ClippingRankSum=-0.329;DB;DP=443;FS=0.613;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=3.315;NEGATIVE_TRAIN_SITE;QD=8.41;ReadPosRankSum=0.164;SOR=0.610;VQSLOD=-3.453e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:298,144:442:99:3756,0,10951 -chr6 57372374 rs68090917 CT C 3672.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.835;ClippingRankSum=0.028;DB;DP=420;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=0;MQRankSum=0.217;POSITIVE_TRAIN_SITE;QD=8.74;ReadPosRankSum=0.275;SOR=0.674;VQSLOD=-1.464e-01;culprit=DP GT:AD:DP:GQ:PL 0/1:274,132:406:99:3710,0,8968 -chr6 57372436 rs9382771 G C 4364.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=4.675;ClippingRankSum=0.150;DB;DP=201;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=-2.890;NEGATIVE_TRAIN_SITE;QD=21.72;ReadPosRankSum=0.305;SOR=1.373;VQSLOD=-1.610e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:74,127:201:99:4393,0,2326 -chr6 57372437 rs79221898 C T 2323.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-9.294;ClippingRankSum=-0.543;DB;DP=202;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.44;MQ0=0;MQRankSum=0.030;QD=11.50;ReadPosRankSum=0.294;SOR=0.345;VQSLOD=0.165;culprit=FS GT:AD:DP:GQ:PL 0/1:123,79:202:99:2352,0,4259 -chr6 57372456 rs35141035 AT A 952.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.481;ClippingRankSum=0.386;DB;DP=149;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.01;MQ0=0;MQRankSum=-1.225;POSITIVE_TRAIN_SITE;QD=6.39;ReadPosRankSum=0.325;SOR=0.544;VQSLOD=3.61;culprit=FS GT:AD:DP:GQ:PL 0/1:65,50:115:99:990,0,1228 -chr6 57372480 rs79601039 A G 1090.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.462;ClippingRankSum=-0.042;DB;DP=82;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.03;MQ0=0;MQRankSum=0.276;QD=13.30;ReadPosRankSum=1.108;SOR=0.482;VQSLOD=3.82;culprit=FS GT:AD:DP:GQ:PL 0/1:46,36:82:99:1119,0,1889 -chr6 57372502 rs9349872 G A 894.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.559;ClippingRankSum=-0.640;DB;DP=44;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.08;MQ0=0;MQRankSum=-3.815;QD=20.34;ReadPosRankSum=-0.166;SOR=0.990;VQSLOD=0.816;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:19,25:44:99:923,0,664 -chr6 57372510 rs77697887 T G 453.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.557;ClippingRankSum=0.318;DB;DP=38;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=47.12;MQ0=0;MQRankSum=-3.102;QD=11.94;ReadPosRankSum=-1.226;SOR=0.307;VQSLOD=0.504;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:24,14:38:99:482,0,966 -chr6 57372514 rs77868044 T C 425.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.126;ClippingRankSum=0.397;DB;DP=32;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=48.03;MQ0=0;MQRankSum=-1.547;QD=13.31;ReadPosRankSum=-1.389;SOR=0.260;VQSLOD=2.80;culprit=FS GT:AD:DP:GQ:PL 0/1:21,11:32:99:454,0,927 -chr6 57372523 rs10706124 TG T 235.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.127;ClippingRankSum=0.381;DB;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=48.16;MQ0=0;MQRankSum=-3.433;POSITIVE_TRAIN_SITE;QD=8.42;ReadPosRankSum=1.704;SOR=0.169;VQSLOD=2.42;culprit=FS GT:AD:DP:GQ:PL 0/1:20,8:28:99:273,0,858 -chr6 57372526 rs10635932 C CTTTA 238.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.250;ClippingRankSum=1.472;DB;DP=26;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=48.24;MQ0=0;MQRankSum=-3.139;POSITIVE_TRAIN_SITE;QD=9.18;ReadPosRankSum=1.694;SOR=0.202;VQSLOD=2.74;culprit=FS GT:AD:DP:GQ:PL 0/1:18,8:26:99:276,0,816 -chr6 57372583 rs9367754 C T 93.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.754;ClippingRankSum=-0.937;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.17;MQ0=0;MQRankSum=-0.937;QD=13.40;ReadPosRankSum=0.000;SOR=0.941;VQSLOD=4.53;culprit=FS GT:AD:DP:GQ:PL 0/1:3,4:7:99:122,0,108 -chr6 57372611 rs9382772 C T 32.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-1.026;QD=8.19;ReadPosRankSum=0.000;SOR=0.693;VQSLOD=3.39;culprit=QD GT:AD:DP:GQ:PL 0/1:2,2:4:61:61,0,77 -chr6 57374364 rs75332238 C T 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:34:40,0,34 -chr6 57379671 rs4573085 C G 43.78 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.727;QD=10.95;ReadPosRankSum=0.727;SOR=0.916;VQSLOD=4.49;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:24:72,0,24 -chr6 57379715 rs2894901 T G 98.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;QD=24.51;SOR=1.609;VQSLOD=5.93;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:126,12,0 -chr6 57379745 rs9476056 G A 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=7.66;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 57384745 rs75634578 T C 40.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=20.37;SOR=0.693;VQSLOD=6.95;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 57385801 rs4715735 A G 39.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=19.87;SOR=0.693;VQSLOD=6.75;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0 -chr6 57386904 rs149764231 GAGA G 43.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.58;ReadPosRankSum=-0.736;SOR=2.225;VQSLOD=2.50;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 -chr6 57389299 rs375498702 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57390094 rs12203268 T C 12.06 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:25:40,0,25 -chr6 57390107 rs200901455 CATCTGTT C 40.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=47.12;MQ0=0;MQRankSum=-1.026;QD=10.18;ReadPosRankSum=0.000;SOR=0.693;VQSLOD=5.20;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,78 -chr6 57390124 rs56102916 G C 111.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=27.76;SOR=0.693;VQSLOD=5.73;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:139,12,0 -chr6 57390134 rs75555855 C T 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=47.12;MQ0=0;MQRankSum=-1.026;QD=6.69;ReadPosRankSum=1.026;SOR=0.693 GT:AD:DP:GQ:PL 0/1:2,2:4:55:55,0,78 -chr6 57390168 rs78919924 C T 29.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=9.93;ReadPosRankSum=0.804;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:27:58,0,27 -chr6 57392874 rs927195 C T 110.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.720;QD=18.46;ReadPosRankSum=0.000;SOR=0.368;VQSLOD=4.73;culprit=FS GT:AD:DP:GQ:PL 0/1:2,4:6:61:139,0,61 -chr6 57392913 rs927194 T C 103.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;ClippingRankSum=-1.638;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=1.368;POSITIVE_TRAIN_SITE;QD=12.97;ReadPosRankSum=-0.922;SOR=0.693;VQSLOD=6.21;culprit=FS GT:AD:DP:GQ:PL 0/1:4,4:8:99:132,0,222 -chr6 57392921 rs62398963 T A 88.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.312;ClippingRankSum=-1.157;DB;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-0.231;QD=6.83;ReadPosRankSum=-0.386;SOR=0.223;VQSLOD=3.71;culprit=QD GT:AD:DP:GQ:PL 0/1:9,4:13:99:117,0,346 -chr6 57392963 rs927193 T C 531.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.951;ClippingRankSum=-0.110;DB;DP=29;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=0.680;QD=18.34;ReadPosRankSum=-0.811;SOR=0.906;VQSLOD=3.89;culprit=FS GT:AD:DP:GQ:PL 0/1:13,16:29:99:560,0,435 -chr6 57393029 rs77090024 T A 813.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=3.045;ClippingRankSum=0.061;DB;DP=76;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-4.889;NEGATIVE_TRAIN_SITE;QD=10.71;ReadPosRankSum=2.576;SOR=0.201;VQSLOD=-3.073e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:52,24:76:99:842,0,2229 -chr6 57393034 rs75127850 G T 1008.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-5.248;ClippingRankSum=0.023;DB;DP=86;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.50;MQ0=0;MQRankSum=-5.580;NEGATIVE_TRAIN_SITE;QD=11.73;ReadPosRankSum=1.286;SOR=0.216;VQSLOD=-3.258e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:58,28:86:99:1037,0,2424 -chr6 57393040 rs74756458 A T 1158.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.499;ClippingRankSum=-1.753;DB;DP=96;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.21;MQ0=0;MQRankSum=-5.165;NEGATIVE_TRAIN_SITE;QD=12.07;ReadPosRankSum=1.667;SOR=0.229;VQSLOD=-3.001e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:64,32:96:99:1187,0,2672 -chr6 57393054 rs75725892 G A 1341.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=8.421;ClippingRankSum=0.555;DB;DP=120;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.42;MQ0=0;MQRankSum=-4.298;NEGATIVE_TRAIN_SITE;QD=11.18;ReadPosRankSum=1.283;SOR=1.179;VQSLOD=-2.209e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:81,39:120:99:1370,0,3620 -chr6 57393074 rs73752376 A G 1772.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=7.296;ClippingRankSum=0.236;DB;DP=171;FS=3.973;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=0;MQRankSum=-2.664;NEGATIVE_TRAIN_SITE;QD=10.37;ReadPosRankSum=0.650;SOR=1.329;VQSLOD=-1.602e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:121,50:171:99:1801,0,5032 -chr6 57393092 rs73752377 T A 2197.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=2.298;ClippingRankSum=0.412;DB;DP=234;FS=2.430;MLEAC=1;MLEAF=0.500;MQ=56.70;MQ0=0;MQRankSum=-2.781;NEGATIVE_TRAIN_SITE;QD=9.39;ReadPosRankSum=-0.722;SOR=0.915;VQSLOD=-1.964e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:164,70:234:99:2226,0,6218 -chr6 57393125 rs927192 A G 7635.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=5.292;ClippingRankSum=-0.772;DB;DP=356;FS=5.930;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=0;MQRankSum=0.055;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=21.45;ReadPosRankSum=-0.840;SOR=0.430;VQSLOD=-2.175e-01;culprit=DP GT:AD:DP:GQ:PL 0/1:129,227:356:99:7664,0,3693 -chr6 57393160 rs76686926 G A 2805.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.132;ClippingRankSum=0.139;DB;DP=395;FS=1.817;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=0;MQRankSum=-1.496;NEGATIVE_TRAIN_SITE;QD=7.10;ReadPosRankSum=0.029;SOR=0.592;VQSLOD=-2.787e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:278,117:395:99:2834,0,8784 -chr6 57393199 rs2397502 C A 3769.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-6.119;ClippingRankSum=1.716;DB;DP=344;FS=1.419;MLEAC=1;MLEAF=0.500;MQ=58.31;MQ0=0;MQRankSum=2.244;NEGATIVE_TRAIN_SITE;QD=10.96;ReadPosRankSum=0.093;SOR=0.606;VQSLOD=-1.342e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:226,118:344:99:3798,0,8416 -chr6 57393216 rs2397503 G T 6455.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-7.047;ClippingRankSum=0.677;DB;DP=273;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.46;MQ0=0;MQRankSum=-1.274;NEGATIVE_TRAIN_SITE;QD=23.65;ReadPosRankSum=0.802;SOR=0.672;VQSLOD=-1.677e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:112,161:273:99:6484,0,4010 -chr6 57393222 rs111989160 A G 2124.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=6.075;ClippingRankSum=0.447;DB;DP=254;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=-0.081;NEGATIVE_TRAIN_SITE;QD=8.37;ReadPosRankSum=1.798;SOR=0.705;VQSLOD=-1.470e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:191,63:254:99:2153,0,7932 -chr6 57393228 rs112156516 G A 2056.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=7.272;ClippingRankSum=-0.141;DB;DP=242;FS=2.168;MLEAC=1;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=0.518;NEGATIVE_TRAIN_SITE;QD=8.50;ReadPosRankSum=2.889;SOR=1.002;VQSLOD=-1.477e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:182,60:242:99:2085,0,7456 -chr6 57393278 rs75909609 T C 978.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=7.163;ClippingRankSum=1.948;DB;DP=126;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.86;MQ0=0;MQRankSum=0.294;QD=7.77;ReadPosRankSum=0.566;SOR=0.428;VQSLOD=1.81;culprit=QD GT:AD:DP:GQ:PL 0/1:93,33:126:99:1007,0,3194 -chr6 57393323 rs12198995 T C 122.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.995;ClippingRankSum=-0.894;DB;DP=63;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.03;MQ0=0;MQRankSum=-1.012;QD=1.95;ReadPosRankSum=0.953;SOR=0.033;VQSLOD=0.768;culprit=QD GT:AD:DP:GQ:PL 0/1:54,9:63:99:151,0,2049 -chr6 57393329 rs76564922 G T 491.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.488;ClippingRankSum=-0.148;DB;DP=58;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.67;MQ0=0;MQRankSum=1.018;QD=8.48;ReadPosRankSum=0.478;SOR=0.145;VQSLOD=3.43;culprit=QD GT:AD:DP:GQ:PL 0/1:42,16:58:99:520,0,1666 -chr6 57393337 rs200714656 T TA 779.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.011;ClippingRankSum=0.247;DB;DP=47;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.61;MQ0=0;MQRankSum=-1.517;POSITIVE_TRAIN_SITE;QD=16.59;ReadPosRankSum=-0.957;SOR=0.446;VQSLOD=5.50;culprit=FS GT:AD:DP:GQ:PL 0/1:27,20:47:99:817,0,1052 -chr6 57393338 rs2397504 T A 1418.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.401;ClippingRankSum=0.911;DB;DP=45;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=-1.809;NEGATIVE_TRAIN_SITE;QD=31.53;ReadPosRankSum=-1.578;SOR=2.059;VQSLOD=-2.208e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:12,33:45:99:1447,0,396 -chr6 57393350 rs2397505 G A 577.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.397;ClippingRankSum=-0.510;DB;DP=37;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.72;MQ0=0;MQRankSum=-2.800;QD=15.62;ReadPosRankSum=-1.686;SOR=0.395;VQSLOD=1.10;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:22,15:37:99:606,0,861 -chr6 57393407 rs374979361 C T 67.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.683;ClippingRankSum=-0.573;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.248;QD=7.53;ReadPosRankSum=-0.248;SOR=0.283;VQSLOD=4.48;culprit=QD GT:AD:DP:GQ:PL 0/1:6,3:9:96:96,0,194 -chr6 57393519 rs62398965 A G 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=7.50;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 57393716 rs2397508 G A 53.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.87;SOR=2.303;VQSLOD=7.44;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 57394939 rs11963080 C T 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57395058 rs12202626 T C 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.37;SOR=2.303;VQSLOD=7.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 57395077 rs12195527 C G 61.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.87;SOR=2.303;VQSLOD=7.52;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:89,6,0 -chr6 57395396 rs74519885 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57396165 rs6924765 G A 52.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=3.82;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:78:81,0,78 -chr6 57396173 rs79246915 G T 52.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=-0.736;SOR=0.223;VQSLOD=4.76;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:78:81,0,78 -chr6 57397866 rs57276498 T TA 68.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;ClippingRankSum=0.000;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.82;MQ0=0;MQRankSum=-0.720;POSITIVE_TRAIN_SITE;QD=11.46;ReadPosRankSum=0.720;SOR=1.329;VQSLOD=5.96;culprit=FS GT:AD:DP:GQ:PL 0/1:2,4:6:38:106,0,38 -chr6 57397944 rs7770986 A G 201.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.659;ClippingRankSum=-0.183;DB;DP=34;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.28;MQ0=0;MQRankSum=0.183;QD=5.93;ReadPosRankSum=-0.386;SOR=0.392;VQSLOD=2.50;culprit=QD GT:AD:DP:GQ:PL 0/1:26,8:34:99:230,0,866 -chr6 57397982 rs7771127 C A 876.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.945;ClippingRankSum=-0.215;DB;DP=57;FS=3.087;MLEAC=1;MLEAF=0.500;MQ=56.94;MQ0=0;MQRankSum=-1.269;QD=15.38;ReadPosRankSum=0.567;SOR=0.197;VQSLOD=1.24;culprit=FS GT:AD:DP:GQ:PL 0/1:29,28:57:99:905,0,992 -chr6 57398008 rs7771257 C T 1863.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-6.114;ClippingRankSum=-0.432;DB;DP=91;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.21;MQ0=0;MQRankSum=-1.126;QD=20.48;ReadPosRankSum=-0.093;SOR=0.232;VQSLOD=3.03;culprit=FS GT:AD:DP:GQ:PL 0/1:44,46:90:99:1892,0,1700 -chr6 57398009 rs7771114 A G 1863.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=5.944;ClippingRankSum=0.703;DB;DP=92;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.26;MQ0=0;MQRankSum=-3.030;POSITIVE_TRAIN_SITE;QD=20.26;ReadPosRankSum=-0.203;SOR=0.241;VQSLOD=3.10;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:44,47:91:99:1892,0,1700 -chr6 57398028 rs67286646 TG T 832.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.812;ClippingRankSum=-0.912;DB;DP=148;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.11;MQ0=0;MQRankSum=0.437;POSITIVE_TRAIN_SITE;QD=5.63;ReadPosRankSum=-0.426;SOR=0.853;VQSLOD=3.92;culprit=FS GT:AD:DP:GQ:PL 0/1:107,40:147:99:870,0,4153 -chr6 57398047 rs76081480 A C 1782.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=7.353;ClippingRankSum=-0.762;DB;DP=191;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.74;MQ0=0;MQRankSum=-2.177;NEGATIVE_TRAIN_SITE;QD=9.33;ReadPosRankSum=-1.084;SOR=0.701;VQSLOD=-1.736e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:127,63:190:99:1811,0,4583 -chr6 57398058 rs7771283 C G 1588.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.421;ClippingRankSum=0.238;DB;DP=230;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=1.141;NEGATIVE_TRAIN_SITE;QD=6.91;ReadPosRankSum=-1.687;SOR=0.435;VQSLOD=-2.531e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:168,61:229:99:1617,0,5971 -chr6 57398081 rs7753294 T G 5599.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=8.745;ClippingRankSum=0.077;DB;DP=263;FS=27.103;MLEAC=1;MLEAF=0.500;MQ=54.71;MQ0=0;MQRankSum=-4.145;NEGATIVE_TRAIN_SITE;QD=21.29;ReadPosRankSum=2.243;SOR=3.663;VQSLOD=-1.976e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:103,159:262:99:5628,0,3075 -chr6 57398117 rs139574925 T TA 2948.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.101;ClippingRankSum=1.493;DB;DP=361;FS=2.214;MLEAC=1;MLEAF=0.500;MQ=54.59;MQ0=0;MQRankSum=-1.420;NEGATIVE_TRAIN_SITE;QD=8.17;ReadPosRankSum=-1.614;SOR=0.901;VQSLOD=-2.236e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:262,99:361:99:2986,0,10807 -chr6 57398118 rs147643173 G T 2951.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-8.611;ClippingRankSum=0.472;DB;DP=366;FS=1.357;MLEAC=1;MLEAF=0.500;MQ=54.39;MQ0=0;MQRankSum=-1.610;NEGATIVE_TRAIN_SITE;QD=8.06;ReadPosRankSum=-1.741;SOR=0.841;VQSLOD=-2.741e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:265,101:366:99:2980,0,10921 -chr6 57398154 rs80081867 T C 9900.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.712;ClippingRankSum=-1.351;DB;DP=417;FS=3.795;MLEAC=1;MLEAF=0.500;MQ=52.44;MQ0=0;MQRankSum=-5.322;NEGATIVE_TRAIN_SITE;QD=23.74;ReadPosRankSum=0.785;SOR=1.039;VQSLOD=-2.613e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:170,247:417:99:9929,0,6569 -chr6 57398157 rs9476080 A G 10031.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=11.939;ClippingRankSum=-0.670;DB;DP=420;FS=5.630;MLEAC=1;MLEAF=0.500;MQ=52.56;MQ0=0;MQRankSum=-6.161;NEGATIVE_TRAIN_SITE;QD=23.89;ReadPosRankSum=1.335;SOR=1.089;VQSLOD=-2.877e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:174,246:420:99:10060,0,6871 -chr6 57398163 rs9476081 A G 9691.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-5.386;ClippingRankSum=-0.317;DB;DP=428;FS=7.782;MLEAC=1;MLEAF=0.500;MQ=52.95;MQ0=0;MQRankSum=-7.057;NEGATIVE_TRAIN_SITE;QD=22.64;ReadPosRankSum=2.150;SOR=1.207;VQSLOD=-3.250e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:182,246:428:99:9720,0,6877 -chr6 57398186 rs147954160 G GA 3146.73 VQSRTrancheINDEL99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.394;ClippingRankSum=0.081;DB;DP=466;FS=0.612;MLEAC=1;MLEAF=0.500;MQ=53.38;MQ0=0;MQRankSum=-5.529;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=6.75;ReadPosRankSum=-0.584;SOR=0.648;VQSLOD=-3.838e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:331,119:450:99:3184,0,13464 -chr6 57398201 rs62398997 T C 9311.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.718;ClippingRankSum=0.323;DB;DP=477;FS=1.130;MLEAC=1;MLEAF=0.500;MQ=53.38;MQ0=0;MQRankSum=-2.722;NEGATIVE_TRAIN_SITE;QD=19.52;ReadPosRankSum=0.869;SOR=0.576;VQSLOD=-2.548e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:235,242:477:99:9340,0,8506 -chr6 57398207 rs71214816 G T 3201.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.739;ClippingRankSum=0.609;DB;DP=476;FS=3.961;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=0;MQRankSum=-5.623;NEGATIVE_TRAIN_SITE;QD=6.73;ReadPosRankSum=0.211;SOR=0.475;VQSLOD=-3.396e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:358,113:471:99:3230,0,14267 -chr6 57398226 rs77436138 T G 5638.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=6.880;ClippingRankSum=1.585;DB;DP=474;FS=4.176;MLEAC=1;MLEAF=0.500;MQ=55.11;MQ0=0;MQRankSum=-0.678;NEGATIVE_TRAIN_SITE;QD=11.90;ReadPosRankSum=-1.594;SOR=0.924;VQSLOD=-2.787e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:202,185:387:99:5667,0,7682 -chr6 57398264 rs62398998 A G 10505.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=7.800;ClippingRankSum=0.363;DB;DP=483;FS=5.181;MLEAC=1;MLEAF=0.500;MQ=56.66;MQ0=0;MQRankSum=-3.599;NEGATIVE_TRAIN_SITE;QD=21.75;ReadPosRankSum=1.128;SOR=0.919;VQSLOD=-2.719e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:185,297:482:99:10534,0,5426 -chr6 57398270 rs62398999 C T 3777.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-8.082;ClippingRankSum=1.817;DB;DP=482;FS=4.566;MLEAC=1;MLEAF=0.500;MQ=56.75;MQ0=0;MQRankSum=-2.615;NEGATIVE_TRAIN_SITE;QD=7.84;ReadPosRankSum=0.627;SOR=1.059;VQSLOD=-3.182e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:338,143:481:99:3806,0,12584 -chr6 57398335 rs4715745 A T 7297.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.878;ClippingRankSum=-0.623;DB;DP=391;FS=18.280;MLEAC=1;MLEAF=0.500;MQ=56.94;MQ0=0;MQRankSum=-1.096;NEGATIVE_TRAIN_SITE;QD=18.66;ReadPosRankSum=0.479;SOR=1.573;VQSLOD=-1.998e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:151,240:391:99:7326,0,4341 -chr6 57398385 rs11455120 A AT 2033.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.004;ClippingRankSum=-0.159;DB;DP=270;FS=2.505;MLEAC=1;MLEAF=0.500;MQ=57.95;MQ0=0;MQRankSum=1.708;POSITIVE_TRAIN_SITE;QD=7.53;ReadPosRankSum=2.608;SOR=1.265;VQSLOD=-3.154e-01;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:165,71:236:99:2071,0,7214 -chr6 57398395 rs78658694 A T 1426.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=5.633;ClippingRankSum=-0.557;DB;DP=246;FS=2.513;MLEAC=1;MLEAF=0.500;MQ=58.16;MQ0=0;MQRankSum=-1.385;NEGATIVE_TRAIN_SITE;QD=5.80;ReadPosRankSum=2.107;SOR=1.287;VQSLOD=-2.484e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:170,67:237:99:1455,0,7359 -chr6 57398412 rs6937166 A G 1614.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=5.113;ClippingRankSum=0.840;DB;DP=201;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=0.045;NEGATIVE_TRAIN_SITE;QD=8.03;ReadPosRankSum=-0.110;SOR=0.142;VQSLOD=-1.257e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:145,56:201:99:1643,0,5481 -chr6 57398491 rs6937368 C T 90.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.276;ClippingRankSum=0.170;DB;DP=40;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-0.019;QD=2.27;ReadPosRankSum=-0.511;SOR=0.039;VQSLOD=1.26;culprit=QD GT:AD:DP:GQ:PL 0/1:34,6:40:99:119,0,1359 -chr6 57398503 rs4388290 A G 387.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.279;ClippingRankSum=-0.151;DB;DP=36;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=-0.319;QD=10.77;ReadPosRankSum=-0.319;SOR=0.239;VQSLOD=2.63;culprit=FS GT:AD:DP:GQ:PL 0/1:24,12:36:99:416,0,1055 -chr6 57398517 rs4400219 C A 314.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.503;ClippingRankSum=0.370;DB;DP=31;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=-0.196;QD=10.15;ReadPosRankSum=0.849;SOR=0.173;VQSLOD=3.45;culprit=FS GT:AD:DP:GQ:PL 0/1:22,9:31:99:343,0,999 -chr6 57398587 rs4506046 A G 226.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.635;ClippingRankSum=-0.831;DB;DP=12;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.977;QD=18.90;ReadPosRankSum=1.977;SOR=1.022;VQSLOD=3.22;culprit=FS GT:AD:DP:GQ:PL 0/1:5,7:12:99:255,0,157 -chr6 57398921 . T C 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:36:40,0,36 -chr6 57398943 rs12203062 C T 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;QD=7.44;ReadPosRankSum=-1.026;SOR=0.693 GT:AD:DP:GQ:PL 0/1:2,2:4:58:58,0,78 -chr6 57404528 rs12528027 A G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57404529 rs71221626 G C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.19;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57404548 rs6934525 T C 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57404559 rs6911998 G T 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57409216 rs487488 T C 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57409238 rs7757807 T G 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57409250 rs28431347 T A 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57409360 rs7775846 A C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.44;MQ0=0;QD=7.26;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57414331 rs522176 A G 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.28;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57414352 rs522107 G T 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57414355 rs577952 G A 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57419091 rs11362490 AG A 32.71 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=16.35;SOR=2.303;VQSLOD=8.34;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 -chr6 57419145 rs482977 T C 101.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.26;SOR=0.693;VQSLOD=7.58;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:129,12,0 -chr6 57419169 rs482916 C T 96.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.09;SOR=1.179;VQSLOD=6.81;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:124,9,0 -chr6 57419203 rs28444227 T A 84.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.09;SOR=1.179;VQSLOD=6.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:112,9,0 -chr6 57419529 rs5011343 C T 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57419548 rs5011342 G A 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.24;SOR=1.609;VQSLOD=4.67;culprit=FS GT:AD:DP:GQ:PL 1/1:0,1:1:6:70,6,0 -chr6 57419564 rs5011341 G A 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.60;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57419593 rs5000703 G T 60.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.09;SOR=1.179;VQSLOD=6.82;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:88,9,0 -chr6 57419621 rs5000702 C A 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.37;SOR=0.693;VQSLOD=7.18;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 57420055 rs973971 A T 47.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=23.87;SOR=0.693;VQSLOD=7.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 57420085 rs10678736 T TGCAATA 43.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.58;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=2.61;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 -chr6 57420331 rs536921 A G 45.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;QD=11.44;ReadPosRankSum=1.026;SOR=0.105;VQSLOD=4.60;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:33:74,0,33 -chr6 57420394 rs3903673 C G 39.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=1.231;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.358;QD=7.95;ReadPosRankSum=1.231;SOR=1.609;VQSLOD=2.43;culprit=QD GT:AD:DP:GQ:PL 0/1:3,2:5:68:68,0,116 -chr6 57429628 rs9476125 T G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.39;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57429632 rs13200513 C A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57429655 rs13200414 A T 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57429863 rs12194179 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57430291 rs12209094 A G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.61;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57430302 rs12195853 G C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=5.78;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57430787 rs9382792 A G 66.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;SOR=1.179;VQSLOD=5.69;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:94,9,0 -chr6 57430868 rs9396334 C T 14.68 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=14.68;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:41,3,0 -chr6 57431267 rs2397534 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57436741 rs6924004 C A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57437720 rs519735 A G 47.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=23.87;SOR=0.693;VQSLOD=6.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 57437853 rs13212334 A G 12.06 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:25:40,0,25 -chr6 57438133 rs1174361 T C 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57438139 rs1174362 C T 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57438156 rs78245671 T C 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.19;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57440169 rs581096 G A 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57440174 rs581102 T C 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57440196 rs581193 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.05;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57440211 rs581228 T A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=9.37;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57442438 rs5005193 C G 60.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.37;SOR=2.303;VQSLOD=7.36;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:88,6,0 -chr6 57442463 rs5005192 T G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.31;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57442488 rs4715782 A G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.25;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57442506 rs5005191 A G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.49;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57442507 rs5005190 A G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.99;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57443228 rs6913239 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57443255 rs1855414 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57447972 rs4715787 T G 53.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.87;SOR=2.303;VQSLOD=6.49;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 57454558 rs9357983 C A 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57454567 rs62399084 A T 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57454589 rs9357984 A G 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.54;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57454920 rs9357986 C T 55.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;QD=18.43;SOR=1.179;VQSLOD=5.05;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:83,9,0 -chr6 57455443 rs7766809 A G 98.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.76;SOR=1.179;VQSLOD=6.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:126,9,0 -chr6 57456136 rs4596481 T C 13.72 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=6.86;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 -chr6 57456931 rs79510351 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57456963 rs75987787 T C 107.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.05;SOR=1.179;VQSLOD=6.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 57456968 rs78473260 G A 107.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.40;SOR=1.179;VQSLOD=6.89;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 -chr6 57457564 rs3805802 A G 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=8.60;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 57461356 rs62399146 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57463643 rs6905367 A G 45.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.87;SOR=2.303;VQSLOD=7.58;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 -chr6 57466787 rs6924157 G C 81.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=-1.231;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.358;QD=16.35;ReadPosRankSum=0.358;SOR=0.223;VQSLOD=5.23;culprit=FS GT:AD:DP:GQ:PL 0/1:2,3:5:59:110,0,59 -chr6 57466812 rs78692044 T A 28.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;ClippingRankSum=0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.04;MQ0=0;MQRankSum=-0.720;QD=4.80;ReadPosRankSum=-0.720;SOR=1.179 GT:AD:DP:GQ:PL 0/1:4,2:6:57:57,0,146 -chr6 57466836 rs11411187 A AC 203.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.067;ClippingRankSum=1.589;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=0.572;POSITIVE_TRAIN_SITE;QD=25.47;ReadPosRankSum=-1.067;SOR=0.693;VQSLOD=5.99;culprit=FS GT:AD:DP:GQ:PL 0/1:2,6:8:57:241,0,57 -chr6 57466844 rs12197381 G A 64.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.573;ClippingRankSum=-0.573;DB;DP=9;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=0.248;QD=7.20;ReadPosRankSum=0.248;SOR=0.045;VQSLOD=0.706;culprit=QD GT:AD:DP:GQ:PL 0/1:6,3:9:93:93,0,212 -chr6 57466871 rs79082382 G A 111.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.793;ClippingRankSum=0.244;DB;DP=12;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=-2.141;QD=9.31;ReadPosRankSum=-0.529;SOR=0.446;VQSLOD=2.61;culprit=FS GT:AD:DP:GQ:PL 0/1:7,5:12:99:140,0,269 -chr6 57466891 rs12210717 A T 431.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.484;ClippingRankSum=-0.698;DB;DP=21;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=0;MQRankSum=-0.611;QD=20.56;ReadPosRankSum=0.349;SOR=0.941;VQSLOD=3.93;culprit=FS GT:AD:DP:GQ:PL 0/1:5,15:20:99:460,0,165 -chr6 57466915 rs12205876 T A 732.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.992;ClippingRankSum=1.449;DB;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.62;MQ0=0;MQRankSum=0.839;QD=26.17;ReadPosRankSum=1.297;SOR=0.402;VQSLOD=2.60;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:8,20:28:99:761,0,252 -chr6 57466922 rs2894917 T C 1572.77 PASS AC=2;AF=1.00;AN=2;DB;DP=36;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.39;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.29;SOR=4.921;VQSLOD=6.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,36:36:99:1601,111,0 -chr6 57466957 rs9885746 C T 515.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=2.903;ClippingRankSum=-0.774;DB;DP=69;FS=3.021;MLEAC=1;MLEAF=0.500;MQ=57.62;MQ0=0;MQRankSum=-0.787;QD=7.47;ReadPosRankSum=-0.192;SOR=0.154;VQSLOD=-3.023e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:49,20:69:99:544,0,2169 -chr6 57466958 rs12212128 A G 1712.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.269;ClippingRankSum=0.064;DB;DP=74;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.81;MQ0=0;MQRankSum=-1.391;QD=23.15;ReadPosRankSum=-0.906;SOR=0.355;VQSLOD=2.47;culprit=FS GT:AD:DP:GQ:PL 0/1:24,50:74:99:1741,0,776 -chr6 57466969 rs12212129 A G 1088.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=6.620;ClippingRankSum=-0.340;DB;DP=83;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.03;MQ0=0;MQRankSum=-0.237;QD=13.12;ReadPosRankSum=-0.386;SOR=0.362;VQSLOD=3.55;culprit=FS GT:AD:DP:GQ:PL 0/1:50,33:83:99:1117,0,1689 -chr6 57466987 rs12205887 T C 1230.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.854;ClippingRankSum=-0.004;DB;DP=98;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=0;MQRankSum=0.575;QD=12.56;ReadPosRankSum=-0.126;SOR=0.389;VQSLOD=3.29;culprit=FS GT:AD:DP:GQ:PL 0/1:58,40:98:99:1259,0,2007 -chr6 57467084 rs9885913 A G 2211.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=4.628;ClippingRankSum=0.293;DB;DP=304;FS=4.869;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=-0.944;NEGATIVE_TRAIN_SITE;QD=7.28;ReadPosRankSum=3.057;SOR=1.014;VQSLOD=-2.572e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:233,71:304:99:2240,0,9850 -chr6 57467093 rs9885916 A G 2301.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=7.069;ClippingRankSum=0.184;DB;DP=312;FS=3.079;MLEAC=1;MLEAF=0.500;MQ=58.58;MQ0=0;MQRankSum=-1.638;NEGATIVE_TRAIN_SITE;QD=7.38;ReadPosRankSum=0.912;SOR=0.918;VQSLOD=-2.342e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:239,73:312:99:2330,0,10451 -chr6 57467100 rs4535533 G C 6947.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.106;ClippingRankSum=-2.135;DB;DP=314;FS=1.422;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=-0.670;NEGATIVE_TRAIN_SITE;QD=22.13;ReadPosRankSum=0.520;SOR=0.800;VQSLOD=-1.704e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:122,192:314:99:6976,0,3683 -chr6 57467107 rs9885751 C T 1881.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=6.859;ClippingRankSum=-1.729;DB;DP=314;FS=5.484;MLEAC=1;MLEAF=0.500;MQ=58.52;MQ0=0;MQRankSum=-1.808;NEGATIVE_TRAIN_SITE;QD=5.99;ReadPosRankSum=0.287;SOR=1.037;VQSLOD=-2.380e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:238,76:314:99:1910,0,9279 -chr6 57467175 rs4406234 A G 2889.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=2.932;ClippingRankSum=-0.383;DB;DP=258;FS=0.469;MLEAC=1;MLEAF=0.500;MQ=58.12;MQ0=0;MQRankSum=0.153;NEGATIVE_TRAIN_SITE;QD=11.20;ReadPosRankSum=4.087;SOR=0.741;VQSLOD=-7.350e-01;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:159,99:258:99:2918,0,5132 -chr6 57467279 rs6459263 T C 1140.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=5.633;ClippingRankSum=1.776;DB;DP=140;FS=4.536;MLEAC=1;MLEAF=0.500;MQ=58.17;MQ0=0;MQRankSum=1.542;NEGATIVE_TRAIN_SITE;QD=8.15;ReadPosRankSum=-0.103;SOR=0.269;VQSLOD=-1.496e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:104,36:140:99:1169,0,4245 -chr6 57467282 rs6459264 T C 1140.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.755;ClippingRankSum=1.153;DB;DP=134;FS=1.319;MLEAC=1;MLEAF=0.500;MQ=58.08;MQ0=0;MQRankSum=1.020;POSITIVE_TRAIN_SITE;QD=8.51;ReadPosRankSum=-0.325;SOR=0.374;VQSLOD=1.58;culprit=QD GT:AD:DP:GQ:PL 0/1:100,34:134:99:1169,0,4245 -chr6 57467303 rs1022846 A G 3478.77 PASS AC=2;AF=1.00;AN=2;DB;DP=90;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.39;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.14;SOR=5.330;VQSLOD=6.74;culprit=QD GT:AD:DP:GQ:PL 1/1:0,90:90:99:3507,271,0 -chr6 57467317 rs4637646 G T 1210.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.996;ClippingRankSum=-0.892;DB;DP=73;FS=4.921;MLEAC=1;MLEAF=0.500;MQ=56.76;MQ0=0;MQRankSum=0.260;QD=16.59;ReadPosRankSum=0.593;SOR=0.140;VQSLOD=0.741;culprit=FS GT:AD:DP:GQ:PL 0/1:40,33:73:99:1239,0,1596 -chr6 57467323 rs4424069 G C 1161.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.993;ClippingRankSum=-0.170;DB;DP=67;FS=4.828;MLEAC=1;MLEAF=0.500;MQ=56.83;MQ0=0;MQRankSum=-0.107;QD=17.34;ReadPosRankSum=0.648;SOR=0.150;VQSLOD=0.857;culprit=FS GT:AD:DP:GQ:PL 0/1:36,31:67:99:1190,0,1431 -chr6 57467456 rs4358625 T G 43.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=14.59;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=1.27;culprit=DP GT:AD:DP:GQ:PL 0/1:1,2:3:31:72,0,31 -chr6 57472201 rs9885694 A G 75.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.054;ClippingRankSum=-0.248;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.573;QD=8.42;ReadPosRankSum=1.683;SOR=0.283;VQSLOD=3.58;culprit=QD GT:AD:DP:GQ:PL 0/1:6,3:9:99:104,0,207 -chr6 57472212 rs9296899 T A 251.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.531;ClippingRankSum=1.531;DB;DP=11;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.377;QD=22.89;ReadPosRankSum=0.382;SOR=1.802;VQSLOD=4.30;culprit=FS GT:AD:DP:GQ:PL 0/1:3,8:11:88:280,0,88 -chr6 57472255 rs9296900 C T 533.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.047;ClippingRankSum=-1.484;DB;DP=20;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=61.07;MQ0=0;MQRankSum=0.524;POSITIVE_TRAIN_SITE;QD=26.69;ReadPosRankSum=-0.786;SOR=2.093;VQSLOD=5.22;culprit=FS GT:AD:DP:GQ:PL 0/1:5,15:20:99:562,0,141 -chr6 57472299 rs9396358 A G 360.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.622;ClippingRankSum=0.811;DB;DP=34;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-0.811;QD=10.61;ReadPosRankSum=-1.460;SOR=0.874;VQSLOD=2.75;culprit=FS GT:AD:DP:GQ:PL 0/1:22,12:34:99:389,0,704 -chr6 57472315 rs9296901 A G 1165.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.692;ClippingRankSum=-0.988;DB;DP=43;FS=2.613;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=0.663;QD=27.11;ReadPosRankSum=-1.151;SOR=0.271;VQSLOD=-5.021e-01;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:12,31:43:99:1194,0,341 -chr6 57472316 rs9382818 G A 458.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.993;ClippingRankSum=-0.012;DB;DP=43;FS=2.578;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=-0.360;QD=10.67;ReadPosRankSum=-1.950;SOR=0.156;VQSLOD=0.405;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:26,17:43:99:487,0,974 -chr6 57472344 rs111230027 A AT 305.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.049;ClippingRankSum=0.230;DB;DP=64;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=1.887;POSITIVE_TRAIN_SITE;QD=4.78;ReadPosRankSum=-0.919;SOR=0.495;VQSLOD=5.04;culprit=FS GT:AD:DP:GQ:PL 0/1:43,17:60:99:343,0,1062 -chr6 57472476 rs9382819 T C 344.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.397;ClippingRankSum=1.197;DB;DP=44;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=-0.718;QD=7.84;ReadPosRankSum=-1.021;SOR=1.226;VQSLOD=1.17;culprit=QD GT:AD:DP:GQ:PL 0/1:30,14:44:99:373,0,1080 -chr6 57472488 rs9382820 C T 419.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.192;ClippingRankSum=0.268;DB;DP=43;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=0.395;QD=9.76;ReadPosRankSum=-1.949;SOR=0.836;VQSLOD=2.80;culprit=FS GT:AD:DP:GQ:PL 0/1:28,15:43:99:448,0,1080 -chr6 57472495 rs62400219 C G 263.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.265;ClippingRankSum=-0.448;DB;DP=38;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=-0.215;QD=6.94;ReadPosRankSum=-0.050;SOR=0.481;VQSLOD=2.66;culprit=QD GT:AD:DP:GQ:PL 0/1:28,10:38:99:292,0,1144 -chr6 57472533 rs9367767 T C 332.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.074;ClippingRankSum=-1.122;DB;DP=17;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.80;MQ0=0;MQRankSum=-0.830;QD=19.57;ReadPosRankSum=0.049;SOR=0.330;VQSLOD=4.65;culprit=FS GT:AD:DP:GQ:PL 0/1:7,10:17:99:361,0,224 -chr6 57472534 rs74369127 T C 46.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.197;ClippingRankSum=0.441;DB;DP=17;FS=7.533;MLEAC=1;MLEAF=0.500;MQ=55.80;MQ0=0;MQRankSum=0.189;NEGATIVE_TRAIN_SITE;QD=2.75;ReadPosRankSum=-1.449;SOR=0.010;VQSLOD=-1.589e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:14,3:17:75:75,0,661 -chr6 57474882 rs62400254 A T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.96;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57474896 rs62400255 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.22;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57476586 rs58187447 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57476608 rs57642151 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57479216 rs4530864 T C 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=7.01;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 57482492 rs12197718 T C 39.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=19.87;SOR=2.303;VQSLOD=6.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0 -chr6 57483749 rs9476179 C T 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:35:40,0,35 -chr6 57485342 rs9885648 T C 10.20 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;ClippingRankSum=0.804;DB;DP=2;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.804;QD=5.10;ReadPosRankSum=0.804;SOR=0.693 GT:AD:DP:GQ:PL 0/1:1,1:2:35:38,0,35 -chr6 57485391 rs1853495 T G 15.65 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=15.65;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0 -chr6 57490861 rs11963269 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57490866 rs9885704 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.81;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57491118 rs9885817 T C 47.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=15.92;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.98;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:32:76,0,32 -chr6 57492741 rs79386390 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57492762 rs3805807 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57492776 rs77611141 G T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57493700 rs62404095 T G 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.23;SOR=1.609;VQSLOD=6.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,1:1:6:86,6,0 -chr6 57493709 rs62404096 A G 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.37;SOR=2.303;VQSLOD=6.82;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 57493836 rs62404099 C A 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.37;SOR=2.303;VQSLOD=7.43;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 57495024 rs5003525 A C 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=8.86;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 57495215 rs6939623 T G 13.72 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=13.72;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 -chr6 57495238 rs62404102 T C 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=25.87;SOR=0.693;VQSLOD=5.79;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 57497543 rs6929435 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.11;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57497562 rs76224813 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.26;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57497579 rs73755610 T G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.63;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57498301 rs11754853 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57498324 rs11759488 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57498894 rs3846934 G A 268.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.827;ClippingRankSum=0.059;DB;DP=15;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=-0.884;QD=17.92;ReadPosRankSum=-0.177;SOR=1.112;VQSLOD=4.80;culprit=FS GT:AD:DP:GQ:PL 0/1:6,9:15:99:297,0,200 -chr6 57498944 rs3846935 G C 516.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.291;ClippingRankSum=-0.826;DB;DP=30;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=0.064;QD=17.23;ReadPosRankSum=0.233;SOR=0.784;VQSLOD=4.16;culprit=FS GT:AD:DP:GQ:PL 0/1:12,18:30:99:545,0,370 -chr6 57499042 rs5876654 A AT 87.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.132;ClippingRankSum=-0.570;DB;DP=25;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.219;POSITIVE_TRAIN_SITE;QD=3.51;ReadPosRankSum=-2.324;SOR=0.770;VQSLOD=4.42;culprit=FS GT:AD:DP:GQ:PL 0/1:13,6:19:99:125,0,294 -chr6 57499171 rs3846936 T C 122.78 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;ClippingRankSum=-0.731;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.731;QD=24.56;ReadPosRankSum=-0.731;SOR=1.981;VQSLOD=4.21;culprit=FS GT:AD:DP:GQ:PL 0/1:1,4:5:25:151,0,25 -chr6 57499188 rs2151627 C T 39.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=13.26;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.90;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:28:68,0,28 -chr6 57499196 rs11423601 C CA 24.75 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=63.51;MQ0=0;MQRankSum=0.736;QD=8.25;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:27:62,0,27 -chr6 57499926 rs2397610 A G 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:35:40,0,35 -chr6 57500073 rs62404596 G A 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.37;SOR=2.303;VQSLOD=6.89;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 57500104 rs62404597 G A 64.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=63.51;MQ0=0;QD=21.43;SOR=1.179;VQSLOD=6.59;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:92,9,0 -chr6 57500169 rs6926645 T G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.37;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57500181 rs76287706 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=4.49;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57500197 rs11329134 GA G 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57500204 rs78362714 C T 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57500220 rs4537145 G A 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57500442 rs4540266 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57503123 rs2397930 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57503159 rs3857631 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57503199 rs3996830 T G 35.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=0.000;QD=8.94;ReadPosRankSum=-1.026;SOR=2.303;VQSLOD=4.04;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:64:64,0,64 -chr6 57503231 rs78058710 A G 140.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;QD=29.11;SOR=1.609;VQSLOD=4.81;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:168,12,0 -chr6 57503398 rs4995671 C A 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.37;SOR=0.693;VQSLOD=7.00;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 57503441 rs4995670 T A 94.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.727;QD=23.69;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.42;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:33:123,0,33 -chr6 57503444 rs11343070 AC A 85.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;POSITIVE_TRAIN_SITE;QD=21.43;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=6.25;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:33:123,0,33 -chr6 57507333 rs148428624 C T 47.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.87;SOR=2.303;VQSLOD=6.18;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 57507431 rs139113051 T C 11.83 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=11.83;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0 -chr6 57507846 rs80010809 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57509520 rs62402976 C T 41.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.87;SOR=0.693;VQSLOD=6.49;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 -chr6 57511438 rs5011992 G A 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.44;MQ0=0;QD=18.25;SOR=0.693;VQSLOD=6.11;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 57511528 rs10592385 AATAAC A 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.58;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=6.31;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57511564 rs5011994 G A 50.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.58;MQ0=0;QD=25.37;SOR=0.693;VQSLOD=6.78;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 57511607 rs77590924 C T 14.68 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=70.00;MQ0=0;QD=14.68;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:41,3,0 -chr6 57511894 rs56224263 T TAC 34.71 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=17.35;SOR=2.303;VQSLOD=8.87;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 -chr6 57512108 rs6914896 G A 40.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;QD=10.19;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=4.26;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:69:69,0,71 -chr6 57512340 rs4364484 C T 502.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.633;ClippingRankSum=-0.142;DB;DP=25;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-1.217;QD=20.11;ReadPosRankSum=-0.311;SOR=1.358;VQSLOD=3.52;culprit=FS GT:AD:DP:GQ:PL 0/1:9,16:25:99:531,0,284 -chr6 57512352 rs5001077 A T 198.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.659;ClippingRankSum=0.512;DB;DP=30;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=0.415;QD=6.63;ReadPosRankSum=-0.122;SOR=0.155;VQSLOD=2.84;culprit=QD GT:AD:DP:GQ:PL 0/1:21,8:29:99:227,0,724 -chr6 57512439 rs4294006 T C 1438.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=3.959;ClippingRankSum=0.864;DB;DP=144;FS=7.438;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=-1.071;QD=9.99;ReadPosRankSum=0.578;SOR=0.083;VQSLOD=-7.791e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:95,49:144:99:1467,0,3234 -chr6 57512476 rs4307164 G A 5505.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.662;ClippingRankSum=2.077;DB;DP=241;FS=1.012;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=1.460;NEGATIVE_TRAIN_SITE;QD=22.85;ReadPosRankSum=-2.015;SOR=0.914;VQSLOD=-1.923e+00;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:78,163:241:99:5534,0,2266 -chr6 57512510 rs4294007 T G 13853.77 PASS AC=2;AF=1.00;AN=2;DB;DP=334;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.18;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.11;SOR=4.194;VQSLOD=3.16;culprit=FS GT:AD:DP:GQ:PL 1/1:0,334:334:99:13882,1010,0 -chr6 57512529 rs5001076 C A 3081.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.175;ClippingRankSum=-2.050;DB;DP=368;FS=3.017;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=0;MQRankSum=-0.390;NEGATIVE_TRAIN_SITE;QD=8.37;ReadPosRankSum=0.294;SOR=0.968;VQSLOD=-2.195e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:255,113:368:99:3110,0,8577 -chr6 57512565 rs4294008 T C 9494.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=5.814;ClippingRankSum=0.828;DB;DP=416;FS=5.007;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=2.938;NEGATIVE_TRAIN_SITE;QD=22.82;ReadPosRankSum=-0.668;SOR=1.299;VQSLOD=-2.221e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:138,278:416:99:9523,0,3960 -chr6 57512678 rs4398719 G A 11124.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=2.677;ClippingRankSum=0.517;DB;DP=458;FS=4.405;MLEAC=1;MLEAF=0.500;MQ=56.48;MQ0=0;MQRankSum=3.775;NEGATIVE_TRAIN_SITE;QD=24.29;ReadPosRankSum=-0.757;SOR=1.082;VQSLOD=-2.409e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:129,325:454:99:11153,0,3458 -chr6 57512711 rs5001484 G C 5059.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=6.115;ClippingRankSum=-0.961;DB;DP=421;FS=6.509;MLEAC=1;MLEAF=0.500;MQ=53.04;MQ0=0;MQRankSum=1.438;NEGATIVE_TRAIN_SITE;QD=12.02;ReadPosRankSum=0.324;SOR=1.225;VQSLOD=-1.980e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:267,138:405:99:5035,0,6158 -chr6 57512718 rs5001483 T A 4671.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.870;ClippingRankSum=0.336;DB;DP=406;FS=3.080;MLEAC=1;MLEAF=0.500;MQ=52.12;MQ0=0;MQRankSum=0.364;NEGATIVE_TRAIN_SITE;QD=11.51;ReadPosRankSum=0.365;SOR=1.044;VQSLOD=-1.109e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:274,131:405:99:4700,0,11219 -chr6 57512740 . CTGTTTT C 1777.73 VQSRTrancheINDEL99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.374;ClippingRankSum=0.035;DP=356;FS=2.783;MLEAC=1;MLEAF=0.500;MQ=49.57;MQ0=0;MQRankSum=-7.250;NEGATIVE_TRAIN_SITE;QD=4.99;ReadPosRankSum=-0.198;SOR=0.328;VQSLOD=-3.212e+00;culprit=DP GT:AD:DP:GQ:PL 0/1:286,64:350:99:1815,0,11798 -chr6 57512775 rs7773110 T G 5490.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-5.254;ClippingRankSum=-0.905;DB;DP=233;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=44.06;MQ0=0;MQRankSum=-4.463;NEGATIVE_TRAIN_SITE;QD=23.57;ReadPosRankSum=-3.464;SOR=1.179;VQSLOD=-2.396e+00;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:92,138:230:99:5519,0,3342 -chr6 57512779 rs76296076 G T 5369.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.880;ClippingRankSum=-0.404;DB;DP=218;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=42.59;MQ0=0;MQRankSum=-5.088;NEGATIVE_TRAIN_SITE;QD=24.63;ReadPosRankSum=-3.913;SOR=1.132;VQSLOD=-2.613e+00;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:89,129:218:99:5398,0,3366 -chr6 57512787 . T TCACCAAGGC 4709.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=4.158;ClippingRankSum=1.208;DP=186;FS=3.774;MLEAC=1;MLEAF=0.500;MQ=39.95;MQ0=0;MQRankSum=-6.907;QD=25.32;ReadPosRankSum=-2.737;SOR=2.176;VQSLOD=-1.452e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:78,108:186:99:4747,0,3127 -chr6 57512788 . T TTA 4547.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-6.353;ClippingRankSum=-0.603;DP=171;FS=3.354;MLEAC=1;MLEAF=0.500;MQ=40.57;MQ0=0;MQRankSum=-7.416;QD=26.59;ReadPosRankSum=-1.258;SOR=1.878;VQSLOD=-9.837e-01;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:79,92:171:99:4585,0,3055 -chr6 57512792 rs372064495 T C 3372.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=7.455;ClippingRankSum=-0.198;DB;DP=157;FS=3.151;MLEAC=1;MLEAF=0.500;MQ=40.80;MQ0=0;MQRankSum=-6.089;NEGATIVE_TRAIN_SITE;QD=21.48;ReadPosRankSum=-0.528;SOR=1.733;VQSLOD=-1.961e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:76,81:157:99:3401,0,3097 -chr6 57512793 rs368894562 AATT A 3279.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=7.041;ClippingRankSum=-0.005;DB;DP=158;FS=3.066;MLEAC=1;MLEAF=0.500;MQ=41.17;MQ0=0;MQRankSum=-7.628;QD=20.76;ReadPosRankSum=-0.270;SOR=1.670;VQSLOD=-9.290e-01;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:78,80:158:99:3317,0,3097 -chr6 57512825 rs72880943 C T 1989.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.227;ClippingRankSum=-1.068;DB;DP=102;FS=3.096;MLEAC=1;MLEAF=0.500;MQ=44.73;MQ0=0;MQRankSum=-6.811;NEGATIVE_TRAIN_SITE;QD=19.51;ReadPosRankSum=0.098;SOR=1.704;VQSLOD=-2.269e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:50,52:102:99:2018,0,1929 -chr6 57512826 rs7752845 A G 1989.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=6.619;ClippingRankSum=1.207;DB;DP=100;FS=3.098;MLEAC=1;MLEAF=0.500;MQ=45.30;MQ0=0;MQRankSum=-6.799;NEGATIVE_TRAIN_SITE;QD=19.90;ReadPosRankSum=0.336;SOR=1.706;VQSLOD=-2.241e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:49,51:100:99:2018,0,1929 -chr6 57512841 rs78256005 A G 630.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.056;ClippingRankSum=-0.094;DB;DP=79;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=46.16;MQ0=0;MQRankSum=-4.822;NEGATIVE_TRAIN_SITE;QD=7.98;ReadPosRankSum=-1.275;SOR=0.455;VQSLOD=-3.272e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:58,21:79:99:659,0,2392 -chr6 57512850 rs77911716 C G 547.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.371;ClippingRankSum=-0.636;DB;DP=72;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=46.71;MQ0=0;MQRankSum=-4.402;NEGATIVE_TRAIN_SITE;QD=7.61;ReadPosRankSum=-1.021;SOR=0.357;VQSLOD=-2.865e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:55,17:72:99:576,0,2261 -chr6 57512874 rs71214002 G A 206.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.499;ClippingRankSum=-0.194;DB;DP=49;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.30;MQ0=0;MQRankSum=-1.846;QD=4.22;ReadPosRankSum=1.072;SOR=0.058;VQSLOD=0.727;culprit=QD GT:AD:DP:GQ:PL 0/1:40,9:49:99:235,0,1573 -chr6 57512889 rs75351177 C T 149.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.464;ClippingRankSum=-0.226;DB;DP=38;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.38;MQ0=0;MQRankSum=-2.862;QD=3.94;ReadPosRankSum=-1.167;SOR=0.061;VQSLOD=-8.131e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:31,7:38:99:178,0,1252 -chr6 57512893 rs77348569 C T 175.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.044;ClippingRankSum=0.000;DB;DP=34;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.45;MQ0=0;MQRankSum=-2.215;QD=5.17;ReadPosRankSum=-0.852;SOR=0.078;VQSLOD=0.483;culprit=QD GT:AD:DP:GQ:PL 0/1:27,7:34:99:204,0,1222 -chr6 57512902 rs77563921 G A 112.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.759;ClippingRankSum=0.900;DB;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.17;MQ0=0;MQRankSum=-1.860;QD=4.03;ReadPosRankSum=-1.140;SOR=0.061;VQSLOD=0.509;culprit=QD GT:AD:DP:GQ:PL 0/1:23,5:28:99:141,0,951 -chr6 57512903 rs75209982 C A 112.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.939;ClippingRankSum=-1.560;DB;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.17;MQ0=0;MQRankSum=-2.939;QD=4.03;ReadPosRankSum=-1.500;SOR=0.061;VQSLOD=-8.813e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:23,5:28:99:141,0,951 -chr6 57512906 rs77519815 T A 337.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.628;ClippingRankSum=1.732;DB;DP=27;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=48.72;MQ0=0;MQRankSum=-3.289;QD=12.51;ReadPosRankSum=-2.536;SOR=0.317;VQSLOD=-8.036e-01;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:17,10:27:99:366,0,726 -chr6 57512916 rs140176282 A AT 70.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.765;ClippingRankSum=-0.191;DB;DP=22;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.71;MQ0=0;MQRankSum=-1.244;QD=3.22;ReadPosRankSum=-0.670;SOR=0.039;VQSLOD=4.77;culprit=FS GT:AD:DP:GQ:PL 0/1:19,3:22:99:108,0,828 -chr6 57513042 rs76730673 C T 87.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=0;QD=29.09;SOR=1.179;VQSLOD=6.60;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:115,9,0 -chr6 57514007 rs4712214 A G 66.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;SOR=1.179;VQSLOD=7.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:94,9,0 -chr6 57514048 rs79485395 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57517722 rs75802839 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=40.87;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.43;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57517733 rs80270590 T A 96.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.10;MQ0=0;QD=32.09;SOR=2.833;VQSLOD=6.48;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:124,9,0 -chr6 57517777 rs76191741 A G 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=47.71;MQ0=0;MQRankSum=1.026;QD=3.96;ReadPosRankSum=0.000;SOR=0.693 GT:AD:DP:GQ:PL 0/1:2,2:4:37:48,0,37 -chr6 57517837 rs79522959 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.28;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57517838 rs1853506 A G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=7.00;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57517853 rs76412158 A T 10.90 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.90;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:37,3,0 -chr6 57518157 rs4993255 T C 62.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.95;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 57519294 rs5017411 C G 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.17;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57519302 rs79076980 T C 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57519303 rs74656916 A G 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57519820 rs7744217 T C 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.63;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57521340 rs73755643 C G 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57521352 rs74795344 A C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.08;SOR=1.609;VQSLOD=6.03;culprit=FS GT:AD:DP:GQ:PL 1/1:0,1:1:6:90,6,0 -chr6 57521365 rs76281818 G T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.15;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57521370 rs61198018 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.32;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57522688 rs76632457 T C 24.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=8.26;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:53,0,33 -chr6 57522722 rs80202467 G T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57522729 rs76599881 G A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=5.83;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57522740 rs78027687 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=5.91;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57522743 rs72880950 G A 52.78 PASS AC=1;AF=0.500;AN=2;DB;DP=2;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;MQ0=0;QD=26.39;SOR=0.693;VQSLOD=7.37;culprit=FS GT:AD:DP:GQ:PL 0/1:0,2:2:26:81,0,26 -chr6 57522745 rs79247610 A C 52.78 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=3.84;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:26:81,0,26 -chr6 57526215 rs5019459 T C 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57526220 rs5019458 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.27;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57526231 rs5019457 A G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.03;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57526585 rs62405765 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.18;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57526610 rs4370353 C T 52.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.16;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 -chr6 57527149 rs77487282 A C 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.37;SOR=0.693;VQSLOD=7.86;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 57528643 rs4989228 G A 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:34:40,0,34 -chr6 57529061 rs4580853 C T 46.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=23.37;SOR=0.693;VQSLOD=7.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:74,6,0 -chr6 57529121 rs4236160 A C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57531762 rs2894929 A C 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.96;MQ0=0;QD=6.20;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57531763 rs4537146 G A 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.96;MQ0=0;QD=6.20;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57536087 rs77762742 T G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57536105 rs77828016 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57538839 rs78941520 C T 43.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=14.59;ReadPosRankSum=0.736;SOR=0.223;VQSLOD=4.60;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:32:72,0,32 -chr6 57538866 rs80259399 C T 49.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=0.000;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;QD=12.44;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=4.77;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,118 -chr6 57538867 rs75525472 A G 49.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;QD=12.44;ReadPosRankSum=0.000;SOR=0.693;VQSLOD=4.75;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,118 -chr6 57538878 rs62405823 G A 86.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=-0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;QD=21.69;ReadPosRankSum=-0.727;SOR=0.916;VQSLOD=4.39;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:29:115,0,29 -chr6 57539231 rs73753049 C T 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;ClippingRankSum=0.804;DB;DP=2;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.804;QD=5.56;ReadPosRankSum=0.804;SOR=1.447 GT:AD:DP:GQ:PL 0/1:1,1:2:34:39,0,34 -chr6 57539244 rs77110690 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.36;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57539245 rs150830310 G A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.83;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57539260 rs73753050 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57539457 rs62405831 G T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.69;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57539460 rs35133381 AT A 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=8.63;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57539480 rs2498202 T A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=6.95;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57544039 rs2498209 C G 60.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.09;SOR=1.179;VQSLOD=7.23;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:88,9,0 -chr6 57546228 rs12212539 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.61;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57546230 rs77288943 G A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.02;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57546234 rs12205399 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.35;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57546244 rs79029147 C G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.40;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57546251 rs78287808 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=32.99;SOR=1.609;VQSLOD=6.28;culprit=FS GT:AD:DP:GQ:PL 1/1:0,1:1:6:90,6,0 -chr6 57546252 rs74936228 G A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=30.52;SOR=1.609;VQSLOD=6.97;culprit=FS GT:AD:DP:GQ:PL 1/1:0,1:1:6:90,6,0 -chr6 57546590 rs1853496 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57547418 rs76051348 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57547428 rs76625067 C G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.04;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57549247 rs2476489 C G 16.63 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=16.63;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:43,3,0 -chr6 57550746 rs74923423 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57550797 rs78408847 G T 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.18;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 -chr6 57556582 rs2397904 C T 14.68 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=14.68;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:41,3,0 -chr6 57556703 rs2397905 G T 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.37;SOR=0.693;VQSLOD=7.30;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 57556977 rs113627621 T C 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.35;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57556995 rs113330746 A G 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57557004 rs4425585 C T 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57560942 rs3903831 C G 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57560949 rs4097974 T C 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57562969 rs77727649 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57564830 rs78356131 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.07;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57564831 rs77336271 G A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.64;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57564861 rs6932761 T C 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.87;SOR=0.693;VQSLOD=6.77;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 57565509 rs11965356 T G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57570509 rs78347797 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57570530 rs6903247 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57574113 rs5008152 G A 71.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 -chr6 57574138 rs5008153 T A 61.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.43;SOR=1.179;VQSLOD=6.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 -chr6 57576825 rs73755103 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57576836 rs73755104 T G 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=6.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57576845 rs73755105 C G 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57595707 rs72871580 T C 52.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=0.736;QD=17.59;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=4.61;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 -chr6 57595709 rs72871582 C T 52.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=-0.736;QD=17.59;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=4.48;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:36:81,0,36 -chr6 57595723 rs75919230 C G 83.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.727;ClippingRankSum=-0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=0.727;QD=20.94;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.77;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:33:112,0,33 -chr6 57595732 rs72871584 G T 83.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=0.727;QD=20.94;ReadPosRankSum=-0.727;SOR=0.916;VQSLOD=4.48;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:33:112,0,33 -chr6 57595770 rs73756249 A G 34.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=0.000;QD=8.69;ReadPosRankSum=1.026;SOR=2.303;VQSLOD=4.24;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:37:63,0,37 -chr6 57595781 rs73457550 G A 33.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=0.000;QD=8.44;ReadPosRankSum=1.026;SOR=2.303;VQSLOD=3.90;culprit=QD GT:AD:DP:GQ:PL 0/1:2,2:4:37:62,0,37 -chr6 57595820 rs73756251 T G 76.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=0.727;QD=19.19;ReadPosRankSum=0.727;SOR=0.446;VQSLOD=4.66;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:29:105,0,29 -chr6 57595832 rs77557182 T C 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;ClippingRankSum=0.804;DB;DP=2;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.804;QD=5.56;ReadPosRankSum=0.804;SOR=1.447 GT:AD:DP:GQ:PL 0/1:1,1:2:39:39,0,39 -chr6 57595845 rs76008427 A T 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57597257 rs72871594 A T 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=25.87;SOR=0.693;VQSLOD=7.04;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 57597260 rs72871595 A T 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=30.27;SOR=1.609;VQSLOD=6.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,1:1:6:79,6,0 -chr6 57603832 rs80257130 A T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.47;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57603839 rs147344208 A AT 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=5.92;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57603845 rs72873407 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=7.34;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57606933 rs73757604 T C 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.37;SOR=2.303;VQSLOD=7.85;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 57606965 rs74644238 T G 66.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=22.09;SOR=1.179;VQSLOD=6.18;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:94,9,0 -chr6 57606996 rs73459287 G C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57607035 rs73757606 G C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.07;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57607044 rs73757607 A G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.28;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 57607068 rs72873457 C T 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57607074 rs4360139 G C 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 57608079 rs73459299 A C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57612661 . G A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57618295 rs5876690 G GA 25.72 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=12.86;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:62,6,0 -chr6 57673397 rs7765475 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57686962 rs140945786 G T 100.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.754;ClippingRankSum=1.754;DB;DP=7;FS=15.441;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.550;POSITIVE_TRAIN_SITE;QD=14.40;ReadPosRankSum=0.937;SOR=3.221;VQSLOD=0.651;culprit=FS GT:AD:DP:GQ:PL 0/1:3,4:7:99:129,0,102 -chr6 57699097 rs6459305 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57710858 rs149357140 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57711844 rs143767848 A T 49.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=8.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 57723952 rs11295509 CA C 37.25 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=12.42;SOR=1.179;VQSLOD=5.67;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:74,9,0 -chr6 57732063 . C A 12.13 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=3.03;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:17:40,0,17 -chr6 57737999 rs142093663 G A 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=27.87;SOR=0.693;VQSLOD=6.23;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 57738613 . C T 20.78 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.39;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:48,6,0 -chr6 57785184 rs116169256 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57826827 . TA T 24.72 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.24;MQ0=0;QD=12.36;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 -chr6 57841273 rs188364530 C T 1364.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.628;ClippingRankSum=0.296;DB;DP=85;FS=7.134;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=1.622;POSITIVE_TRAIN_SITE;QD=16.06;ReadPosRankSum=-0.110;SOR=0.843;VQSLOD=1.24;culprit=FS GT:AD:DP:GQ:PL 0/1:38,47:85:99:1393,0,1205 -chr6 57841320 rs140816261 G T 1315.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.878;ClippingRankSum=-0.287;DB;DP=83;FS=5.670;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=-0.132;POSITIVE_TRAIN_SITE;QD=15.85;ReadPosRankSum=-0.515;SOR=1.312;VQSLOD=1.62;culprit=FS GT:AD:DP:GQ:PL 0/1:40,43:83:99:1344,0,1358 -chr6 57841627 rs149540211 AC A 954.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.085;ClippingRankSum=0.306;DB;DP=80;FS=3.046;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=1.819;QD=11.93;ReadPosRankSum=-1.129;SOR=0.798;VQSLOD=0.740;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:42,36:78:99:992,0,1172 -chr6 57842518 rs149985050 G T 70.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.754;ClippingRankSum=0.000;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=10.11;ReadPosRankSum=0.937;SOR=0.495;VQSLOD=5.83;culprit=FS GT:AD:DP:GQ:PL 0/1:4,3:7:99:99,0,144 -chr6 57843574 rs115026909 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57857856 rs3000344 T C 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.19;MQ0=0;QD=21.37;SOR=0.693;VQSLOD=7.46;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 57972306 rs55752203 TG T 24.72 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.84;MQ0=0;QD=12.36;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 -chr6 57977600 rs115553313 C T 97.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.43;SOR=1.179;VQSLOD=8.27;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:125,9,0 -chr6 57977640 rs4960490 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 57998262 rs9476413 T C 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=6.67;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 58028492 rs147632909 C A 37.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=0.000;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=9.44;ReadPosRankSum=0.000;SOR=2.303;VQSLOD=5.34;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:66:66,0,74 -chr6 58039789 rs9382925 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 58165037 . T G 62.74 PASS AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.84;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 58165039 . A G 62.74 PASS AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=31.37;SOR=0.693;VQSLOD=6.45;culprit=DP GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 58165065 . GT G 53.70 PASS AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=5.77;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 58173632 rs114670858 T G 20.78 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=10.39;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:48,6,0 -chr6 58246055 rs6918567 T C 2357.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.591;ClippingRankSum=-0.427;DB;DP=249;FS=6.315;MLEAC=1;MLEAF=0.500;MQ=50.51;MQ0=0;MQRankSum=-11.921;POSITIVE_TRAIN_SITE;QD=9.47;ReadPosRankSum=2.161;SOR=1.112;VQSLOD=-3.174e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:179,69:248:99:2386,0,8176 -chr6 58246056 rs6930828 G A 2357.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.659;ClippingRankSum=0.056;DB;DP=250;FS=5.251;MLEAC=1;MLEAF=0.500;MQ=50.59;MQ0=0;MQRankSum=-11.878;QD=9.43;ReadPosRankSum=-0.007;SOR=1.079;VQSLOD=-4.553e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:179,70:249:99:2386,0,8176 -chr6 58246143 rs6931014 G A 3997.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;ClippingRankSum=-0.730;DB;DP=326;FS=0.849;MLEAC=1;MLEAF=0.500;MQ=49.42;MQ0=0;MQRankSum=-4.926;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=12.26;ReadPosRankSum=3.641;SOR=0.631;VQSLOD=-1.659e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:186,138:324:99:4026,0,5840 -chr6 58250570 rs9500243 A T 402.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.537;ClippingRankSum=0.754;DB;DP=40;FS=8.709;MLEAC=1;MLEAF=0.500;MQ=50.10;MQ0=0;MQRankSum=0.698;POSITIVE_TRAIN_SITE;QD=10.07;ReadPosRankSum=0.112;SOR=0.032;VQSLOD=1.36;culprit=FS GT:AD:DP:GQ:PL 0/1:25,15:40:99:431,0,789 -chr6 58252949 . A G 37.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.322;ClippingRankSum=-0.684;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=36.30;MQ0=0;MQRankSum=-0.684;QD=4.72;ReadPosRankSum=0.322;SOR=0.368;VQSLOD=3.52;culprit=QD GT:AD:DP:GQ:PL 0/1:5,3:8:66:66,0,144 -chr6 58260059 rs74657950 G A 177.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.067;ClippingRankSum=0.058;DB;DP=15;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.79;MQ0=0;MQRankSum=-2.025;QD=11.85;ReadPosRankSum=0.984;SOR=0.582;VQSLOD=2.97;culprit=FS GT:AD:DP:GQ:PL 0/1:8,7:15:99:206,0,240 -chr6 58260138 rs62464086 A G 246.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.547;ClippingRankSum=-0.921;DB;DP=43;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=-2.308;QD=5.74;ReadPosRankSum=0.921;SOR=0.569;VQSLOD=0.439;culprit=QD GT:AD:DP:GQ:PL 0/1:28,14:42:99:275,0,785 -chr6 58263609 rs4079740 A G 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.231;ClippingRankSum=-1.231;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=44.65;MQ0=0;MQRankSum=-1.231;QD=3.57;ReadPosRankSum=0.358;SOR=0.446 GT:AD:DP:GQ:PL 0/1:3,2:5:46:46,0,99 -chr6 58263871 rs6588681 T C 325.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.892;ClippingRankSum=-0.055;DB;DP=33;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.21;MQ0=0;MQRankSum=-2.022;QD=9.87;ReadPosRankSum=1.730;SOR=0.941;VQSLOD=1.68;culprit=FS GT:AD:DP:GQ:PL 0/1:19,14:33:99:354,0,577 -chr6 58263932 rs1810425 G A 548.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.642;ClippingRankSum=-0.644;DB;DP=42;FS=1.298;MLEAC=1;MLEAF=0.500;MQ=56.18;MQ0=0;MQRankSum=-0.407;QD=13.07;ReadPosRankSum=-0.223;SOR=1.002;VQSLOD=1.43;culprit=FS GT:AD:DP:GQ:PL 0/1:23,18:41:99:577,0,758 -chr6 58263952 rs1810426 A G 478.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.162;ClippingRankSum=-0.058;DB;DP=46;FS=2.893;MLEAC=1;MLEAF=0.500;MQ=56.38;MQ0=0;MQRankSum=1.471;QD=10.41;ReadPosRankSum=0.683;SOR=1.251;VQSLOD=1.23;culprit=QD GT:AD:DP:GQ:PL 0/1:27,18:45:99:507,0,927 -chr6 58265128 rs9391382 T C 346.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=1.844;ClippingRankSum=-0.596;DB;DP=54;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=43.99;MQ0=0;MQRankSum=-5.275;NEGATIVE_TRAIN_SITE;QD=6.42;ReadPosRankSum=-1.037;SOR=0.793;VQSLOD=-3.620e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:36,18:54:99:375,0,1179 -chr6 58265398 rs17488291 G A 1245.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.662;ClippingRankSum=0.505;DB;DP=89;FS=7.385;MLEAC=1;MLEAF=0.500;MQ=53.47;MQ0=0;MQRankSum=-1.229;POSITIVE_TRAIN_SITE;QD=14.00;ReadPosRankSum=1.648;SOR=1.478;VQSLOD=1.83;culprit=FS GT:AD:DP:GQ:PL 0/1:47,42:89:99:1274,0,1450 -chr6 58265469 . G GTTT 400.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.047;ClippingRankSum=1.203;DP=68;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.92;MQ0=0;MQRankSum=-3.451;QD=5.89;ReadPosRankSum=-0.359;SOR=0.651;VQSLOD=1.97;culprit=FS GT:AD:DP:GQ:PL 0/1:34,19:53:99:438,0,1230 -chr6 58273526 rs4928423 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 58287821 rs9404620 A G 128.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.307;ClippingRankSum=0.876;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=0.729;POSITIVE_TRAIN_SITE;QD=14.31;ReadPosRankSum=0.000;SOR=0.892;VQSLOD=6.42;culprit=FS GT:AD:DP:GQ:PL 0/1:4,5:9:99:157,0,118 -chr6 58294828 rs2012049 C T 129.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.663;ClippingRankSum=-0.251;DB;DP=17;FS=2.884;MLEAC=1;MLEAF=0.500;MQ=51.67;MQ0=0;MQRankSum=-2.161;POSITIVE_TRAIN_SITE;QD=7.63;ReadPosRankSum=-0.151;SOR=1.688;VQSLOD=0.937;culprit=QD GT:AD:DP:GQ:PL 0/1:11,6:17:99:158,0,414 -chr6 58302194 rs693484 T A 47.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=0.693;VQSLOD=8.67;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 58365506 rs60186309 T TA 41.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.85;SOR=0.693;VQSLOD=8.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 -chr6 58447068 rs1224740 A G 1017.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.800;ClippingRankSum=-0.222;DB;DP=64;FS=3.511;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=0.316;POSITIVE_TRAIN_SITE;QD=15.90;ReadPosRankSum=-0.356;SOR=1.296;VQSLOD=3.10;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:32,32:64:99:1046,0,1021 -chr6 58465552 rs1224802 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.51;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 58490384 rs7770844 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 58693830 rs2343003 A C 60.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=2.303;VQSLOD=9.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:88,6,0 -chr6 58735978 rs2343014 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 58776289 rs4357163 T G 186.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=2.202;ClippingRankSum=0.775;DB;DP=26;FS=2.192;MLEAC=1;MLEAF=0.500;MQ=33.30;MQ0=0;MQRankSum=-1.085;QD=7.18;ReadPosRankSum=0.837;SOR=1.460;VQSLOD=0.168;culprit=QD GT:AD:DP:GQ:PL 0/1:13,10:23:99:215,0,418 -chr6 58776318 rs9986349 A G 261.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.368;ClippingRankSum=-0.152;DB;DP=22;FS=2.098;MLEAC=1;MLEAF=0.500;MQ=32.68;MQ0=0;MQRankSum=-0.684;QD=11.90;ReadPosRankSum=-0.304;SOR=0.243;VQSLOD=1.18;culprit=QD GT:AD:DP:GQ:PL 0/1:11,9:20:99:290,0,435 -chr6 58776319 rs9638012 C T 871.77 PASS AC=2;AF=1.00;AN=2;DB;DP=22;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=32.68;MQ0=0;QD=28.76;SOR=2.093;VQSLOD=5.62;culprit=FS GT:AD:DP:GQ:PL 1/1:0,20:20:60:900,60,0 -chr6 58776352 rs4317432 T C 267.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.799;ClippingRankSum=-0.318;DB;DP=17;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.04;MQ0=0;MQRankSum=-0.847;QD=15.75;ReadPosRankSum=-1.059;SOR=0.653;VQSLOD=4.28;culprit=FS GT:AD:DP:GQ:PL 0/1:7,9:16:99:296,0,314 -chr6 58776411 rs9638013 A G 364.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.887;ClippingRankSum=-1.415;DB;DP=18;FS=2.846;MLEAC=1;MLEAF=0.500;MQ=28.44;MQ0=0;MQRankSum=-0.283;QD=20.26;ReadPosRankSum=0.962;SOR=0.148;VQSLOD=1.19;culprit=QD GT:AD:DP:GQ:PL 0/1:4,13:17:99:393,0,132 -chr6 58776442 rs9638019 T C 491.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.786;ClippingRankSum=0.381;DB;DP=25;FS=2.593;MLEAC=1;MLEAF=0.500;MQ=35.87;MQ0=0;MQRankSum=-0.498;QD=19.67;ReadPosRankSum=0.088;SOR=1.863;VQSLOD=1.35;culprit=QD GT:AD:DP:GQ:PL 0/1:10,14:24:99:520,0,292 -chr6 58776542 rs4524636 G A 45.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.367;ClippingRankSum=0.115;DB;DP=64;FS=1.496;MLEAC=1;MLEAF=0.500;MQ=48.96;MQ0=0;MQRankSum=0.136;NEGATIVE_TRAIN_SITE;QD=0.72;ReadPosRankSum=-0.073;SOR=1.179;VQSLOD=-1.126e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:54,8:62:74:74,0,1805 -chr6 58776555 rs4928523 T C 742.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.227;ClippingRankSum=-0.403;DB;DP=63;FS=9.224;MLEAC=1;MLEAF=0.500;MQ=49.77;MQ0=0;MQRankSum=0.433;QD=11.79;ReadPosRankSum=1.884;SOR=1.229;VQSLOD=4.000e-03;culprit=FS GT:AD:DP:GQ:PL 0/1:36,25:61:99:771,0,1202 -chr6 58776592 rs9377908 A G 222.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.650;ClippingRankSum=-0.434;DB;DP=74;FS=1.153;MLEAC=1;MLEAF=0.500;MQ=54.28;MQ0=0;MQRankSum=0.889;NEGATIVE_TRAIN_SITE;QD=3.01;ReadPosRankSum=0.918;SOR=0.460;VQSLOD=-9.187e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:58,14:72:99:251,0,2116 -chr6 58776745 rs9632507 C T 3168.77 PASS AC=2;AF=1.00;AN=2;DB;DP=80;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.29;MQ0=0;QD=32.18;SOR=0.927;VQSLOD=5.45;culprit=FS GT:AD:DP:GQ:PL 1/1:0,74:74:99:3197,226,0 -chr6 58776782 rs9632508 A T 3215.77 PASS AC=2;AF=1.00;AN=2;DB;DP=83;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.76;MQ0=0;QD=30.10;SOR=0.887;VQSLOD=5.64;culprit=FS GT:AD:DP:GQ:PL 1/1:0,77:77:99:3244,240,0 -chr6 58776802 rs4401693 T G 670.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.160;ClippingRankSum=-0.171;DB;DP=80;FS=3.349;MLEAC=1;MLEAF=0.500;MQ=54.82;MQ0=0;MQRankSum=2.069;QD=8.38;ReadPosRankSum=0.137;SOR=1.112;VQSLOD=-5.951e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:49,25:74:99:699,0,1658 -chr6 58776855 rs4928552 A G 1233.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.182;ClippingRankSum=0.370;DB;DP=79;FS=1.923;MLEAC=1;MLEAF=0.500;MQ=54.95;MQ0=0;MQRankSum=1.187;QD=15.62;ReadPosRankSum=-0.469;SOR=0.872;VQSLOD=1.36;culprit=DP GT:AD:DP:GQ:PL 0/1:35,38:73:99:1262,0,1231 -chr6 58776887 rs113904338 A G 105.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=3.374;ClippingRankSum=-1.479;DB;DP=74;FS=1.493;MLEAC=1;MLEAF=0.500;MQ=54.73;MQ0=0;MQRankSum=1.286;NEGATIVE_TRAIN_SITE;QD=1.43;ReadPosRankSum=1.305;SOR=1.159;VQSLOD=-1.368e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:59,8:67:99:134,0,2069 -chr6 58776958 rs4562168 A T 38.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.772;ClippingRankSum=1.153;DB;DP=68;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.56;MQ0=0;MQRankSum=0.582;QD=0.57;ReadPosRankSum=1.725;SOR=0.941;VQSLOD=0.880;culprit=QD GT:AD:DP:GQ:PL 0/1:58,7:65:67:67,0,2198 -chr6 58776965 rs9632509 C T 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.964;ClippingRankSum=-1.381;DB;DP=72;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.35;MQ0=0;MQRankSum=1.202;QD=0.26;ReadPosRankSum=1.441;SOR=0.796 GT:AD:DP:GQ:PL 0/1:62,7:69:47:47,0,2234 -chr6 58776982 rs9632510 G T 1497.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-3.267;ClippingRankSum=0.065;DB;DP=67;FS=1.041;MLEAC=1;MLEAF=0.500;MQ=51.72;MQ0=0;MQRankSum=-0.411;QD=22.35;ReadPosRankSum=-0.887;SOR=0.510;VQSLOD=-2.878e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:19,46:65:99:1526,0,547 -chr6 58776984 rs56092323 A T 39.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.000;ClippingRankSum=0.603;DB;DP=67;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=51.72;MQ0=0;MQRankSum=1.386;QD=0.59;ReadPosRankSum=1.323;SOR=0.787;VQSLOD=0.978;culprit=QD GT:AD:DP:GQ:PL 0/1:58,7:65:68:68,0,2352 -chr6 58777039 rs28781680 G A 376.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.782;ClippingRankSum=-0.924;DB;DP=63;FS=4.123;MLEAC=1;MLEAF=0.500;MQ=46.06;MQ0=0;MQRankSum=1.682;QD=5.98;ReadPosRankSum=-0.766;SOR=1.179;VQSLOD=-5.013e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:47,16:63:99:405,0,1853 -chr6 58777056 rs9654654 G T 772.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.293;ClippingRankSum=0.839;DB;DP=64;FS=5.150;MLEAC=1;MLEAF=0.500;MQ=45.93;MQ0=0;MQRankSum=1.899;QD=12.07;ReadPosRankSum=-0.041;SOR=1.004;VQSLOD=0.153;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:39,25:64:99:801,0,1404 -chr6 58777074 rs4388312 C T 822.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.624;ClippingRankSum=-1.281;DB;DP=65;FS=6.614;MLEAC=1;MLEAF=0.500;MQ=49.69;MQ0=0;MQRankSum=0.164;QD=12.66;ReadPosRankSum=-1.018;SOR=0.612;VQSLOD=0.293;culprit=FS GT:AD:DP:GQ:PL 0/1:34,31:65:99:851,0,1154 -chr6 58777106 rs4610595 A G 643.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.791;ClippingRankSum=1.422;DB;DP=67;FS=5.024;MLEAC=1;MLEAF=0.500;MQ=56.66;MQ0=0;MQRankSum=-0.611;QD=9.61;ReadPosRankSum=0.573;SOR=0.565;VQSLOD=0.035;culprit=QD GT:AD:DP:GQ:PL 0/1:41,26:67:99:672,0,1465 -chr6 58777109 rs9647639 C T 510.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.158;ClippingRankSum=0.783;DB;DP=69;FS=9.064;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=0;MQRankSum=0.783;NEGATIVE_TRAIN_SITE;QD=7.40;ReadPosRankSum=-1.203;SOR=1.679;VQSLOD=-1.890e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:46,23:69:99:539,0,1603 -chr6 58777156 rs4577825 C G 121.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.790;ClippingRankSum=0.330;DB;DP=81;FS=4.661;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=0;MQRankSum=1.120;NEGATIVE_TRAIN_SITE;QD=1.50;ReadPosRankSum=-0.258;SOR=1.196;VQSLOD=-2.068e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:67,11:78:99:150,0,2400 -chr6 58777178 rs9638022 G T 2960.77 PASS AC=2;AF=1.00;AN=2;DB;DP=78;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.64;MQ0=0;QD=28.06;SOR=0.774;VQSLOD=5.10;culprit=FS GT:AD:DP:GQ:PL 1/1:0,75:75:99:2989,229,0 -chr6 58777233 rs4336468 C T 554.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.430;ClippingRankSum=-1.640;DB;DP=65;FS=1.047;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=0.052;QD=8.53;ReadPosRankSum=0.696;SOR=0.914;VQSLOD=0.514;culprit=QD GT:AD:DP:GQ:PL 0/1:44,19:63:99:583,0,1593 -chr6 58777237 rs4518527 A G 633.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-4.144;ClippingRankSum=0.639;DB;DP=59;FS=5.406;MLEAC=1;MLEAF=0.500;MQ=58.17;MQ0=0;MQRankSum=1.634;QD=10.74;ReadPosRankSum=-0.971;SOR=0.569;VQSLOD=-4.540e-02;culprit=QD GT:AD:DP:GQ:PL 0/1:34,24:58:99:662,0,1277 -chr6 58777276 rs4446588 A C 897.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.100;ClippingRankSum=0.236;DB;DP=62;FS=0.990;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=1.879;QD=14.48;ReadPosRankSum=0.023;SOR=0.662;VQSLOD=0.954;culprit=FS GT:AD:DP:GQ:PL 0/1:32,27:59:99:926,0,946 -chr6 58777295 rs9638023 T C 2798.77 PASS AC=2;AF=1.00;AN=2;DB;DP=67;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.73;MQ0=0;QD=33.48;SOR=0.790;VQSLOD=5.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,63:63:99:2827,196,0 -chr6 58777312 rs9632511 T C 759.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;ClippingRankSum=-1.050;DB;DP=72;FS=11.531;MLEAC=1;MLEAF=0.500;MQ=57.36;MQ0=0;MQRankSum=-1.776;QD=10.55;ReadPosRankSum=0.984;SOR=1.631;VQSLOD=-1.664e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:44,23:67:99:788,0,1478 -chr6 58777366 rs9632513 A G 2731.77 PASS AC=2;AF=1.00;AN=2;DB;DP=68;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.45;MQ0=0;QD=29.84;SOR=0.756;VQSLOD=5.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,64:64:99:2760,199,0 -chr6 58777546 rs9632515 G A 2432.77 PASS AC=2;AF=1.00;AN=2;DB;DP=69;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.61;MQ0=0;QD=30.91;SOR=0.723;VQSLOD=5.57;culprit=FS GT:AD:DP:GQ:PL 1/1:0,67:67:99:2461,201,0 -chr6 58777573 rs9632516 C T 2295.77 VQSRTrancheSNP99.00to99.90 AC=2;AF=1.00;AN=2;BaseQRankSum=-0.251;ClippingRankSum=1.138;DB;DP=66;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.30;MQ0=0;MQRankSum=-0.559;NEGATIVE_TRAIN_SITE;QD=34.78;ReadPosRankSum=1.794;SOR=0.826;VQSLOD=-6.277e-01;culprit=QD GT:AD:DP:GQ:PL 1/1:2,62:64:99:2324,117,0 -chr6 58777583 rs4351287 A G 250.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=2.157;ClippingRankSum=0.238;DB;DP=69;FS=1.199;MLEAC=1;MLEAF=0.500;MQ=55.52;MQ0=0;MQRankSum=-0.221;QD=3.63;ReadPosRankSum=0.648;SOR=0.717;VQSLOD=-7.794e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:52,13:65:99:279,0,1731 -chr6 58777599 . T G 144.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=0.474;ClippingRankSum=-0.957;DP=71;FS=5.022;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=-0.563;NEGATIVE_TRAIN_SITE;QD=2.04;ReadPosRankSum=-0.063;SOR=0.899;VQSLOD=-1.822e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:56,10:66:99:173,0,1929 -chr6 58777775 . A C 471.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.300;ClippingRankSum=0.625;DP=64;FS=1.059;MLEAC=1;MLEAF=0.500;MQ=56.10;MQ0=0;MQRankSum=0.170;QD=7.37;ReadPosRankSum=1.517;SOR=0.904;VQSLOD=0.168;culprit=QD GT:AD:DP:GQ:PL 0/1:40,19:59:99:500,0,1465 -chr6 58777789 rs4296911 T C 850.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.376;ClippingRankSum=-0.201;DB;DP=67;FS=8.737;MLEAC=1;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=0.892;QD=12.70;ReadPosRankSum=-2.082;SOR=0.733;VQSLOD=-2.447e-01;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:35,28:63:99:879,0,1323 -chr6 58777828 rs11211786 G A 652.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.463;ClippingRankSum=-0.018;DB;DP=77;FS=10.707;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=2.081;NEGATIVE_TRAIN_SITE;QD=8.48;ReadPosRankSum=-0.651;SOR=1.322;VQSLOD=-1.674e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:46,26:72:99:681,0,1420 -chr6 58777836 rs9632517 A C 2870.77 PASS AC=2;AF=1.00;AN=2;DB;DP=76;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.16;MQ0=0;QD=28.37;SOR=0.811;VQSLOD=2.74;culprit=FS GT:AD:DP:GQ:PL 1/1:0,70:70:99:2899,214,0 -chr6 58777939 rs9632518 G A 2463.77 PASS AC=2;AF=1.00;AN=2;DB;DP=65;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.89;MQ0=0;QD=25.14;SOR=1.143;VQSLOD=4.33;culprit=FS GT:AD:DP:GQ:PL 1/1:0,62:62:99:2492,187,0 -chr6 58777952 rs4546514 A G 853.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.230;ClippingRankSum=-1.282;DB;DP=63;FS=2.122;MLEAC=1;MLEAF=0.500;MQ=43.01;MQ0=0;MQRankSum=1.134;QD=13.55;ReadPosRankSum=2.245;SOR=0.460;VQSLOD=1.24;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:28,32:60:99:882,0,851 -chr6 58778001 . G A 533.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.458;ClippingRankSum=-0.800;DP=68;FS=0.981;MLEAC=1;MLEAF=0.500;MQ=45.56;MQ0=0;MQRankSum=-0.598;QD=7.85;ReadPosRankSum=0.699;SOR=0.563;VQSLOD=-6.300e-02;culprit=QD GT:AD:DP:GQ:PL 0/1:41,22:63:99:562,0,1296 -chr6 58778019 rs9638027 T G 165.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=2.004;ClippingRankSum=-1.301;DB;DP=72;FS=1.422;MLEAC=1;MLEAF=0.500;MQ=45.92;MQ0=0;MQRankSum=1.339;NEGATIVE_TRAIN_SITE;QD=2.30;ReadPosRankSum=0.522;SOR=1.106;VQSLOD=-1.041e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:56,9:65:99:194,0,2191 -chr6 58778025 rs9638028 A G 2317.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.876;ClippingRankSum=-0.113;DB;DP=72;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.27;MQ0=0;MQRankSum=-0.523;QD=32.19;ReadPosRankSum=0.277;SOR=0.604;VQSLOD=0.716;culprit=FS GT:AD:DP:GQ:PL 0/1:7,60:67:99:2346,0,110 -chr6 58778036 rs9404685 A C 534.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.105;ClippingRankSum=-1.103;DB;DP=69;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=44.49;MQ0=0;MQRankSum=-0.499;QD=7.75;ReadPosRankSum=1.173;SOR=0.668;VQSLOD=2.83;culprit=QD GT:AD:DP:GQ:PL 0/1:38,25:63:99:563,0,1164 -chr6 58778039 rs9638014 G C 2754.77 PASS AC=2;AF=1.00;AN=2;DB;DP=69;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.01;MQ0=0;QD=30.33;SOR=0.790;VQSLOD=5.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,63:63:99:2783,190,0 -chr6 58778081 rs4389792 T G 2804.77 PASS AC=2;AF=1.00;AN=2;DB;DP=66;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.55;MQ0=0;QD=36.83;SOR=0.865;VQSLOD=3.57;culprit=QD GT:AD:DP:GQ:PL 1/1:0,61:61:99:2833,190,0 -chr6 58778082 rs4346876 T C 2759.77 PASS AC=2;AF=1.00;AN=2;DB;DP=66;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.55;MQ0=0;QD=35.85;SOR=0.865;VQSLOD=5.04;culprit=QD GT:AD:DP:GQ:PL 1/1:0,61:61:99:2788,187,0 -chr6 58778100 rs9391506 A T 94.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.077;ClippingRankSum=-0.536;DB;DP=63;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.08;MQ0=0;MQRankSum=-0.098;QD=1.50;ReadPosRankSum=-0.930;SOR=0.801;VQSLOD=0.858;culprit=QD GT:AD:DP:GQ:PL 0/1:48,9:57:99:123,0,1551 -chr6 58778108 rs4308591 G C 2796.77 PASS AC=2;AF=1.00;AN=2;DB;DP=68;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.20;MQ0=0;QD=21.44;SOR=1.092;VQSLOD=3.79;culprit=FS GT:AD:DP:GQ:PL 1/1:0,63:63:99:2825,196,0 -chr6 58778145 rs9500568 T C 228.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.501;ClippingRankSum=0.435;DB;DP=69;FS=1.229;MLEAC=1;MLEAF=0.500;MQ=55.74;MQ0=0;MQRankSum=0.074;QD=3.32;ReadPosRankSum=0.631;SOR=0.425;VQSLOD=-7.171e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:52,13:65:99:257,0,1648 -chr6 58778148 rs12213271 T C 43.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.529;ClippingRankSum=0.210;DB;DP=69;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.74;MQ0=0;MQRankSum=-2.466;NEGATIVE_TRAIN_SITE;QD=0.63;ReadPosRankSum=-1.168;SOR=0.796;VQSLOD=-1.747e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:57,8:65:72:72,0,1899 -chr6 58778190 rs9767581 T G 325.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=2.002;ClippingRankSum=-0.571;DB;DP=71;FS=1.103;MLEAC=1;MLEAF=0.500;MQ=57.28;MQ0=0;MQRankSum=0.860;QD=4.59;ReadPosRankSum=0.340;SOR=0.886;VQSLOD=-4.734e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:52,16:68:99:354,0,1641 -chr6 58778207 rs6588729 G A 2273.77 VQSRTrancheSNP99.00to99.90 AC=2;AF=1.00;AN=2;BaseQRankSum=1.676;ClippingRankSum=-1.397;DB;DP=65;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.24;MQ0=0;MQRankSum=0.950;NEGATIVE_TRAIN_SITE;QD=34.98;ReadPosRankSum=-1.341;SOR=0.236;VQSLOD=-1.078e+00;culprit=QD GT:AD:DP:GQ:PL 1/1:1,61:62:99:2302,182,0 -chr6 58778244 rs6588730 A T 2044.77 PASS AC=2;AF=1.00;AN=2;DB;DP=65;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.41;MQ0=0;QD=31.46;SOR=0.760;VQSLOD=4.48;culprit=FS GT:AD:DP:GQ:PL 1/1:0,60:60:99:2073,180,0 -chr6 58778404 rs6588731 C A 2347.77 PASS AC=2;AF=1.00;AN=2;DB;DP=57;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.80;MQ0=0;QD=32.04;SOR=0.808;VQSLOD=5.86;culprit=FS GT:AD:DP:GQ:PL 1/1:0,53:53:99:2376,160,0 -chr6 58778405 rs6588732 C T 2392.77 PASS AC=2;AF=1.00;AN=2;DB;DP=56;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.66;MQ0=0;QD=27.48;SOR=0.770;VQSLOD=4.38;culprit=FS GT:AD:DP:GQ:PL 1/1:0,52:52:99:2421,163,0 -chr6 58778412 rs6588733 T C 2705.77 PASS AC=2;AF=1.00;AN=2;DB;DP=62;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.42;MQ0=0;QD=34.01;SOR=0.762;VQSLOD=5.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,58:58:99:2734,184,0 -chr6 58778452 rs4928629 A C 970.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.809;ClippingRankSum=-0.744;DB;DP=64;FS=5.099;MLEAC=1;MLEAF=0.500;MQ=55.54;MQ0=0;MQRankSum=2.130;POSITIVE_TRAIN_SITE;QD=15.17;ReadPosRankSum=1.163;SOR=1.249;VQSLOD=1.86;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:29,32:61:99:999,0,986 -chr6 58778456 . G T 154.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.779;ClippingRankSum=-0.534;DP=68;FS=2.839;MLEAC=1;MLEAF=0.500;MQ=55.81;MQ0=0;MQRankSum=1.216;NEGATIVE_TRAIN_SITE;QD=2.28;ReadPosRankSum=0.079;SOR=0.654;VQSLOD=-8.069e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:54,11:65:99:183,0,2074 -chr6 58778482 rs6588734 G A 2628.77 PASS AC=2;AF=1.00;AN=2;DB;DP=64;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.61;MQ0=0;QD=31.77;SOR=0.906;VQSLOD=3.80;culprit=FS GT:AD:DP:GQ:PL 1/1:0,60:60:99:2657,190,0 -chr6 58778519 rs4928633 A G 847.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.545;ClippingRankSum=-1.803;DB;DP=75;FS=6.752;MLEAC=1;MLEAF=0.500;MQ=54.72;MQ0=0;MQRankSum=-1.213;QD=11.30;ReadPosRankSum=0.443;SOR=1.183;VQSLOD=-4.825e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:44,24:68:99:876,0,1700 -chr6 58778530 rs9647643 T C 919.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=3.069;ClippingRankSum=-0.130;DB;DP=71;FS=8.855;MLEAC=1;MLEAF=0.500;MQ=54.76;MQ0=0;MQRankSum=-0.936;QD=12.95;ReadPosRankSum=-0.567;SOR=1.363;VQSLOD=-7.510e-02;culprit=FS GT:AD:DP:GQ:PL 0/1:38,26:64:99:948,0,1688 -chr6 58778531 rs9647644 A C 922.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.990;ClippingRankSum=0.934;DB;DP=70;FS=8.966;MLEAC=1;MLEAF=0.500;MQ=54.68;MQ0=0;MQRankSum=-1.454;QD=13.18;ReadPosRankSum=-0.204;SOR=1.572;VQSLOD=-3.370e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:38,25:63:99:951,0,1651 -chr6 58778577 rs6588735 T A 348.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.086;ClippingRankSum=0.432;DB;DP=70;FS=8.999;MLEAC=1;MLEAF=0.500;MQ=54.75;MQ0=0;MQRankSum=-0.934;NEGATIVE_TRAIN_SITE;QD=4.98;ReadPosRankSum=0.225;SOR=0.956;VQSLOD=-2.510e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:49,13:62:99:377,0,2028 -chr6 58778584 rs6588736 T G 310.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-2.597;ClippingRankSum=0.859;DB;DP=67;FS=2.940;MLEAC=1;MLEAF=0.500;MQ=54.51;MQ0=0;MQRankSum=0.896;QD=4.64;ReadPosRankSum=0.545;SOR=0.275;VQSLOD=-1.432e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:48,12:60:99:339,0,2037 -chr6 58778664 rs112323615 T G 597.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.932;ClippingRankSum=-0.755;DB;DP=68;FS=5.051;MLEAC=1;MLEAF=0.500;MQ=57.08;MQ0=0;MQRankSum=0.959;QD=8.79;ReadPosRankSum=-0.864;SOR=0.980;VQSLOD=-2.673e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:44,22:66:99:626,0,1333 -chr6 58778716 rs7453620 A C 1189.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.027;ClippingRankSum=-0.970;DB;DP=79;FS=6.175;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=-0.769;QD=15.06;ReadPosRankSum=-1.098;SOR=0.261;VQSLOD=0.195;culprit=FS GT:AD:DP:GQ:PL 0/1:36,39:75:99:1218,0,1070 -chr6 58778747 rs12214947 T C 88.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-1.524;ClippingRankSum=-1.054;DB;DP=88;FS=4.622;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=0.705;NEGATIVE_TRAIN_SITE;QD=1.01;ReadPosRankSum=1.189;SOR=0.575;VQSLOD=-2.375e+00;culprit=QD GT:AD:DP:GQ:PL 0/1:72,11:83:99:117,0,2437 -chr6 58778788 rs6651013 T C 3397.77 PASS AC=2;AF=1.00;AN=2;DB;DP=99;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.86;MQ0=0;QD=34.32;SOR=0.976;VQSLOD=4.25;culprit=FS GT:AD:DP:GQ:PL 1/1:0,94:94:99:3426,282,0 -chr6 58778844 rs7452594 C G 898.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=0.445;ClippingRankSum=-0.341;DB;DP=82;FS=12.217;MLEAC=1;MLEAF=0.500;MQ=58.57;MQ0=0;MQRankSum=0.289;QD=10.96;ReadPosRankSum=1.634;SOR=1.334;VQSLOD=-6.564e-01;culprit=FS GT:AD:DP:GQ:PL 0/1:49,29:78:99:927,0,1649 -chr6 58778922 rs6651011 C A 2529.77 VQSRTrancheSNP99.00to99.90 AC=2;AF=1.00;AN=2;BaseQRankSum=1.683;ClippingRankSum=1.147;DB;DP=74;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.77;MQ0=0;MQRankSum=1.586;NEGATIVE_TRAIN_SITE;QD=34.19;ReadPosRankSum=-0.952;SOR=0.246;VQSLOD=-1.389e+00;culprit=FS GT:AD:DP:GQ:PL 1/1:1,70:71:99:2558,204,0 -chr6 58778989 rs6651015 T C 2986.77 PASS AC=2;AF=1.00;AN=2;DB;DP=74;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.71;MQ0=0;QD=37.21;SOR=0.722;VQSLOD=4.76;culprit=QD GT:AD:DP:GQ:PL 1/1:0,69:69:99:3015,208,0 -chr6 58779007 rs6651016 C T 3187.77 PASS AC=2;AF=1.00;AN=2;DB;DP=78;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.13;MQ0=0;QD=33.52;SOR=0.836;VQSLOD=5.60;culprit=FS GT:AD:DP:GQ:PL 1/1:0,73:73:99:3216,223,0 -chr6 58779056 rs6937914 T C 824.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.434;ClippingRankSum=0.011;DB;DP=75;FS=0.903;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-1.194;QD=11.00;ReadPosRankSum=0.535;SOR=0.535;VQSLOD=0.407;culprit=FS GT:AD:DP:GQ:PL 0/1:41,31:72:99:853,0,1368 -chr6 58779089 rs4286808 C A 635.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=2.994;ClippingRankSum=-1.111;DB;DP=63;FS=14.811;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.125;NEGATIVE_TRAIN_SITE;QD=10.09;ReadPosRankSum=0.169;SOR=1.477;VQSLOD=-1.459e+00;culprit=FS GT:AD:DP:GQ:PL 0/1:40,22:62:99:664,0,1572 -chr6 58779097 rs9500231 A G 1804.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-0.594;ClippingRankSum=1.075;DB;DP=68;FS=2.521;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=-0.173;QD=26.54;ReadPosRankSum=0.414;SOR=0.501;VQSLOD=-2.854e-01;culprit=DP GT:AD:DP:GQ:PL 0/1:15,52:67:99:1833,0,403 -chr6 58779308 rs6651018 T C 16.86 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.004;ClippingRankSum=-0.972;DB;DP=51;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.75;MQ0=0;MQRankSum=-0.526;QD=0.33;ReadPosRankSum=0.430;SOR=0.783 GT:AD:DP:GQ:PL 0/1:42,6:48:45:45,0,1235 -chr6 58779328 rs6651019 A G 1227.77 VQSRTrancheSNP99.00to99.90 AC=2;AF=1.00;AN=2;BaseQRankSum=0.974;ClippingRankSum=-1.310;DB;DP=39;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.52;MQ0=0;MQRankSum=0.772;QD=31.48;ReadPosRankSum=1.511;SOR=1.675;VQSLOD=0.201;culprit=FS GT:AD:DP:GQ:PL 1/1:2,35:37:38:1256,38,0 -chr6 58779346 rs4376372 T G 350.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.662;ClippingRankSum=-0.500;DB;DP=32;FS=2.071;MLEAC=1;MLEAF=0.500;MQ=39.86;MQ0=0;MQRankSum=0.460;QD=10.96;ReadPosRankSum=-0.500;SOR=1.292;VQSLOD=1.45;culprit=QD GT:AD:DP:GQ:PL 0/1:18,13:31:99:379,0,605 -chr6 58779375 rs4250419 A G 273.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.795;ClippingRankSum=-0.971;DB;DP=18;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.82;MQ0=0;MQRankSum=-0.442;QD=15.21;ReadPosRankSum=-1.589;SOR=1.781;VQSLOD=3.91;culprit=FS GT:AD:DP:GQ:PL 0/1:9,9:18:99:302,0,370 -chr6 58779376 rs6651020 C T 736.77 PASS AC=2;AF=1.00;AN=2;DB;DP=17;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=30.93;MQ0=0;QD=27.25;SOR=4.294;VQSLOD=5.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,17:17:54:765,54,0 -chr6 58779409 rs4400241 T C 160.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.793;ClippingRankSum=1.461;DB;DP=12;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=32.29;MQ0=0;MQRankSum=0.529;QD=13.40;ReadPosRankSum=1.788;SOR=1.371;VQSLOD=4.57;culprit=FS GT:AD:DP:GQ:PL 0/1:7,5:12:99:189,0,263 -chr6 58779468 rs6651021 A G 83.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=30.90;MQ0=0;MQRankSum=-0.727;QD=20.94;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=4.64;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:28:112,0,28 -chr6 58779499 rs6651022 T C 49.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=-1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=29.00;MQ0=0;MQRankSum=-1.026;QD=12.44;ReadPosRankSum=1.026;SOR=0.693;VQSLOD=4.09;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:54:78,0,54 -chr6 61892431 rs4467815 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 61909056 rs189688252 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 61924395 rs74442497 A C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 61924424 rs149028611 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 61939361 rs76899121 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 61967504 rs704487 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 61967842 rs79961499 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 61984979 . G T 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:34:40,0,34 -chr6 62017935 rs1997843 T C 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=0.693;VQSLOD=9.50;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 62024599 rs1414786 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62027240 rs1074429 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62034435 rs115639864 C T 36.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.988;ClippingRankSum=0.406;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.04;MQ0=0;MQRankSum=0.406;QD=6.13;ReadPosRankSum=-0.406;SOR=0.693;VQSLOD=4.21;culprit=QD GT:AD:DP:GQ:PL 0/1:3,3:6:65:65,0,104 -chr6 62084214 rs3908837 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62114785 rs7742522 T G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62183331 rs2092608 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62183845 rs35300708 C CT 19.75 LowQual AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=6.58;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:56,6,0 -chr6 62198757 rs6916640 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62208255 rs116736672 G A 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.86;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 62217827 rs415716 G T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62220171 rs387256 A T 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 62233173 rs214151 G C 71.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.30;MQ0=0;QD=17.76;SOR=0.693;VQSLOD=5.02;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 -chr6 62236450 rs116060945 A T 18.80 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=9.40;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:46,6,0 -chr6 62252108 rs4598053 C A 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.68;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 62252188 rs67145854 GA G 75.25 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.08;SOR=1.179;VQSLOD=8.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:112,9,0 -chr6 62269382 rs59519746 T C 18.59 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=18.59;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0 -chr6 62269405 rs56095991 G T 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=7.79;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 62290945 rs140805963 G A 44.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=5.79;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:31:73,0,31 -chr6 62294589 rs115452241 T C 55.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=18.43;SOR=1.179;VQSLOD=6.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:83,9,0 -chr6 62316285 rs213776 A C 47.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.026;ClippingRankSum=0.000;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=11.94;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=5.88;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:67:76,0,67 -chr6 62329027 rs201975337 A AT 15.82 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=7.91;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:52,6,0 -chr6 62390916 rs1204114 T C 2091.77 PASS AC=2;AF=1.00;AN=2;DB;DP=56;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.71;SOR=0.765;VQSLOD=6.90;culprit=FS GT:AD:DP:GQ:PL 1/1:0,56:56:99:2120,168,0 -chr6 62413546 rs1204139 A C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62495041 rs78507898 T A 20.78 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.39;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:48,6,0 -chr6 62510310 rs1743448 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62515335 . C A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62532253 rs571607 G C 60.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.37;SOR=0.693;VQSLOD=9.11;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:88,6,0 -chr6 62582748 . G T 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;QD=4.02;ReadPosRankSum=0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:33:40,0,33 -chr6 62604848 . T TTC 69.25 PASS AC=2;AF=1.00;AN=2;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.21;MQ0=0;QD=13.85;SOR=2.303;VQSLOD=5.37;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:9:106,9,0 -chr6 62650334 rs1114027 T A 48.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=8.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 62674103 rs1192455 C T 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=9.36;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 62674110 rs1192454 G A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.92;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 62686434 rs1192430 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62690574 rs1393669 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62706684 rs2102790 C T 48.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=7.03;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 62708691 rs9453889 C A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 62757987 rs9346001 C T 744.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.533;ClippingRankSum=0.028;DB;DP=52;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.661;POSITIVE_TRAIN_SITE;QD=14.32;ReadPosRankSum=1.294;SOR=0.546;VQSLOD=5.40;culprit=FS GT:AD:DP:GQ:PL 0/1:28,24:52:99:773,0,900 -chr6 62886921 rs10455666 C T 184.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.067;ClippingRankSum=-0.572;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.067;POSITIVE_TRAIN_SITE;QD=23.10;ReadPosRankSum=-0.572;SOR=1.863;VQSLOD=6.13;culprit=FS GT:AD:DP:GQ:PL 0/1:2,6:8:59:213,0,59 -chr6 62887031 rs9346218 C T 1086.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.596;ClippingRankSum=1.848;DB;DP=62;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.846;POSITIVE_TRAIN_SITE;QD=17.53;ReadPosRankSum=-0.056;SOR=0.846;VQSLOD=5.07;culprit=FS GT:AD:DP:GQ:PL 0/1:29,33:62:99:1115,0,921 -chr6 62887099 rs6921170 C T 1783.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.393;ClippingRankSum=0.055;DB;DP=121;FS=0.706;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=0.039;POSITIVE_TRAIN_SITE;QD=14.74;ReadPosRankSum=-0.465;SOR=0.841;VQSLOD=2.95;culprit=FS GT:AD:DP:GQ:PL 0/1:60,60:120:99:1812,0,2047 -chr6 62995920 rs16883133 T G 157.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;ClippingRankSum=-0.572;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=19.72;ReadPosRankSum=1.067;SOR=0.693;VQSLOD=6.06;culprit=FS GT:AD:DP:GQ:PL 0/1:2,6:8:55:186,0,55 -chr6 63018890 rs9354897 A G 47.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.76;SOR=1.179;VQSLOD=7.60;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:75,9,0 -chr6 63022153 rs523967 G A 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=2.303;VQSLOD=9.05;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 63022286 rs62414811 G A 58.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.37;SOR=2.303;VQSLOD=8.98;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:86,6,0 -chr6 63046505 rs508263 T C 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.80;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 63104500 rs2814661 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63116886 rs2452472 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63123748 rs2814696 C A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63139149 rs2452463 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63167529 rs2881136 G A 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 63171060 rs17381471 C T 645.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.586;ClippingRankSum=-0.249;DB;DP=71;FS=9.277;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.188;POSITIVE_TRAIN_SITE;QD=9.10;ReadPosRankSum=-0.067;SOR=2.159;VQSLOD=0.690;culprit=QD GT:AD:DP:GQ:PL 0/1:47,24:71:99:674,0,1531 -chr6 63171544 rs648165 A T 113.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;ClippingRankSum=-0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.380;POSITIVE_TRAIN_SITE;QD=18.96;ReadPosRankSum=1.380;SOR=1.329;VQSLOD=6.18;culprit=FS GT:AD:DP:GQ:PL 0/1:2,4:6:62:142,0,62 -chr6 63251196 rs2345983 C T 109.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.937;ClippingRankSum=-0.550;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.62;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=15.68;ReadPosRankSum=-0.550;SOR=0.941;VQSLOD=6.88;culprit=FS GT:AD:DP:GQ:PL 0/1:3,4:7:90:138,0,90 -chr6 63257354 rs9446610 C T 1142.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.489;ClippingRankSum=-0.017;DB;DP=75;FS=1.132;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-0.447;POSITIVE_TRAIN_SITE;QD=15.24;ReadPosRankSum=0.337;SOR=0.935;VQSLOD=3.19;culprit=FS GT:AD:DP:GQ:PL 0/1:38,35:73:99:1171,0,1224 -chr6 63257971 rs6913632 T C 1383.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.999;ClippingRankSum=0.127;DB;DP=63;FS=2.484;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=1.565;POSITIVE_TRAIN_SITE;QD=21.96;ReadPosRankSum=-0.367;SOR=0.382;VQSLOD=1.73;culprit=QD GT:AD:DP:GQ:PL 0/1:19,44:63:99:1412,0,451 -chr6 63258233 rs11447029 C CA 15.85 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.718;ClippingRankSum=-1.371;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=-0.065;QD=0.99;ReadPosRankSum=0.588;SOR=0.160 GT:AD:DP:GQ:PL 0/1:11,4:15:53:53,0,220 -chr6 63290332 rs9351926 C A 41.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=13.92;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=5.99;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:36:70,0,36 -chr6 63309881 rs73762312 G T 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.61;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 63356605 rs4710365 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63357734 rs66885289 CTT C 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=7.46;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 63370591 rs7776261 C A 49.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=8.45;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 63370651 rs7761764 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63394799 rs4131720 C A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63426649 rs2752973 C T 43.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=14.59;ReadPosRankSum=0.736;SOR=2.225;VQSLOD=2.74;culprit=DP GT:AD:DP:GQ:PL 0/1:1,2:3:32:72,0,32 -chr6 63480621 rs6937512 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63508240 rs4710370 A C 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.30;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 63508253 rs4710371 T A 14.68 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=14.68;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:41,3,0 -chr6 63520794 rs7746171 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63522176 rs9352169 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63567509 rs11961562 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63576005 rs55851245 C G 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=0.693;VQSLOD=8.14;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 63584587 rs12207161 G A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.52;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 63584592 rs12208504 G A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=0.693;VQSLOD=8.23;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 63596076 rs7747071 G A 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=8.75;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 63596112 rs4307155 C T 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=7.90;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 63607258 rs10943283 C A 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=9.09;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 63727757 rs9343533 C A 287.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.82;SOR=2.833;VQSLOD=6.93;culprit=FS GT:AD:DP:GQ:PL 1/1:0,8:8:24:316,24,0 -chr6 63730222 rs9352418 G T 61.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.08;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 -chr6 63730266 rs9343536 T C 47.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.87;SOR=0.693;VQSLOD=8.81;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 63733880 rs10943404 G T 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=2.303;VQSLOD=8.55;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 63749658 rs6936280 A G 59.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.87;SOR=2.303;VQSLOD=8.69;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 -chr6 63749860 rs6941288 T C 49.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.87;SOR=0.693;VQSLOD=4.12;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 63753907 rs12208886 A G 62.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=7.60;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 63757242 . G T 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63775888 rs789964 A T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63785384 rs789954 G A 48.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=0.693;VQSLOD=7.80;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 63792401 rs1086295 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63863011 rs57238578 G GGTTGTT 44.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.35;SOR=2.303;VQSLOD=8.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 63874309 rs9343765 G A 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.87;SOR=2.303;VQSLOD=7.35;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 63874499 rs7747081 C T 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=8.58;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 63885713 rs3059784 T TTG 26.71 LowQual AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.71;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:6:63,6,0 -chr6 63885782 rs1020805 T G 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=8.09;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 63902995 rs1847501 G T 1552.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=6.223;ClippingRankSum=0.500;DB;DP=79;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.817;POSITIVE_TRAIN_SITE;QD=19.66;ReadPosRankSum=-0.005;SOR=0.743;VQSLOD=4.99;culprit=FS GT:AD:DP:GQ:PL 0/1:34,45:79:99:1581,0,943 -chr6 63903354 rs16893840 G T 550.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.190;ClippingRankSum=0.804;DB;DP=38;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=0;MQRankSum=-0.219;POSITIVE_TRAIN_SITE;QD=14.49;ReadPosRankSum=0.570;SOR=0.754;VQSLOD=5.91;culprit=FS GT:AD:DP:GQ:PL 0/1:20,18:38:99:579,0,671 -chr6 63903377 rs6914331 G A 1128.77 PASS AC=2;AF=1.00;AN=2;DB;DP=28;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=54.85;MQ0=0;POSITIVE_TRAIN_SITE;QD=22.22;SOR=1.609;VQSLOD=5.16;culprit=FS GT:AD:DP:GQ:PL 1/1:0,28:28:84:1157,84,0 -chr6 63903384 rs2047899 G T 382.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.034;ClippingRankSum=-0.528;DB;DP=28;FS=1.690;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-1.080;POSITIVE_TRAIN_SITE;QD=13.67;ReadPosRankSum=0.345;SOR=0.269;VQSLOD=2.91;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:14,14:28:99:411,0,430 -chr6 63903574 rs142293404 GAAGGAGC G 121.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.754;ClippingRankSum=1.754;DB;DP=8;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=47.12;MQ0=0;MQRankSum=-1.754;QD=15.22;ReadPosRankSum=0.000;SOR=2.494;VQSLOD=0.824;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:3,4:7:99:159,0,331 -chr6 63903606 rs116456502 G A 133.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.720;ClippingRankSum=0.000;DB;DP=6;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=0;MQRankSum=-1.380;POSITIVE_TRAIN_SITE;QD=22.29;ReadPosRankSum=1.231;SOR=3.258;VQSLOD=1.17;culprit=DP GT:AD:DP:GQ:PL 0/1:2,4:6:99:162,0,243 -chr6 63921361 rs4710420 A G 237.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.72;SOR=4.407;VQSLOD=7.22;culprit=FS GT:AD:DP:GQ:PL 1/1:0,8:8:24:266,24,0 -chr6 63921442 rs76273486 G A 318.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.127;ClippingRankSum=-0.433;DB;DP=17;FS=3.274;MLEAC=1;MLEAF=0.500;MQ=51.85;MQ0=0;MQRankSum=2.261;POSITIVE_TRAIN_SITE;QD=18.75;ReadPosRankSum=1.299;SOR=1.981;VQSLOD=1.50;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:8,9:17:99:347,0,251 -chr6 63921456 rs79100944 G A 493.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.628;ClippingRankSum=-0.102;DB;DP=22;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.18;MQ0=0;MQRankSum=1.740;QD=22.44;ReadPosRankSum=1.604;SOR=1.402;VQSLOD=0.390;culprit=FS GT:AD:DP:GQ:PL 0/1:8,14:22:99:522,0,233 -chr6 63921924 rs9359357 A G 278.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.409;ClippingRankSum=-1.184;DB;DP=19;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.85;MQ0=0;MQRankSum=-1.347;QD=14.67;ReadPosRankSum=1.266;SOR=1.609;VQSLOD=3.62;culprit=FS GT:AD:DP:GQ:PL 0/1:10,9:19:99:307,0,291 -chr6 63933615 rs9352684 A T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63937797 rs12526013 T C 105.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.116;ClippingRankSum=-0.735;DB;DP=23;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=41.41;MQ0=0;MQRankSum=-0.385;POSITIVE_TRAIN_SITE;QD=4.60;ReadPosRankSum=0.175;SOR=0.141;VQSLOD=3.69;culprit=QD GT:AD:DP:GQ:PL 0/1:17,6:23:99:134,0,553 -chr6 63937863 rs3925806 T C 119.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.380;ClippingRankSum=0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.720;POSITIVE_TRAIN_SITE;QD=19.96;ReadPosRankSum=0.720;SOR=0.368;VQSLOD=6.05;culprit=FS GT:AD:DP:GQ:PL 0/1:2,4:6:60:148,0,60 -chr6 63937916 rs3925805 A C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 63939795 rs1809272 T C 2647.77 VQSRTrancheSNP99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=-6.907;ClippingRankSum=0.336;DB;DP=202;FS=8.305;MLEAC=1;MLEAF=0.500;MQ=53.46;MQ0=0;MQRankSum=-3.258;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=13.11;ReadPosRankSum=-0.632;SOR=0.350;VQSLOD=-4.749e-01;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:107,93:200:99:2676,0,3595 -chr6 63939829 rs1809271 A T 8543.77 PASS AC=2;AF=1.00;AN=2;DB;DP=238;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.90;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.91;SOR=0.925;VQSLOD=3.77;culprit=QD GT:AD:DP:GQ:PL 1/1:0,237:237:99:8572,713,0 -chr6 63940061 rs4035417 A G 1171.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=2.262;ClippingRankSum=-0.144;DB;DP=64;FS=5.367;MLEAC=1;MLEAF=0.500;MQ=51.76;MQ0=0;MQRankSum=-3.916;NEGATIVE_TRAIN_SITE;QD=18.31;ReadPosRankSum=1.606;SOR=0.207;VQSLOD=-1.900e+00;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:26,38:64:99:1200,0,790 -chr6 63940313 rs6905048 A C 40.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=20.37;SOR=2.303;VQSLOD=6.78;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 -chr6 63969766 rs9352729 A G 60.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.37;SOR=2.303;VQSLOD=7.74;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:88,6,0 -chr6 63990648 rs35296992 A G 956.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.261;ClippingRankSum=-0.057;DB;DP=88;FS=2.946;MLEAC=1;MLEAF=0.500;MQ=59.79;MQ0=0;MQRankSum=-0.678;POSITIVE_TRAIN_SITE;QD=10.87;ReadPosRankSum=-0.582;SOR=0.521;VQSLOD=1.69;culprit=QD GT:AD:DP:GQ:PL 0/1:54,33:87:99:985,0,1782 -chr6 64126837 rs149978231 T TAC 29.71 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;QD=14.85;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:66,6,0 -chr6 64147016 rs144385019 AAGAAAGGGAGAAGGAAAAGAAAGAAAGG A 85.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=39.12;MQ0=0;MQRankSum=-0.727;QD=21.43;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=5.01;culprit=FS GT:AD:DP:GQ:PL 0/1:1,3:4:99:123,0,203 -chr6 64150689 rs10755410 G A 62.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.404;ClippingRankSum=-0.740;DB;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.185;POSITIVE_TRAIN_SITE;QD=4.83;ReadPosRankSum=1.849;SOR=0.582;VQSLOD=4.90;culprit=QD GT:AD:DP:GQ:PL 0/1:9,3:12:91:91,0,260 -chr6 64151093 rs9361767 A G 149.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.572;ClippingRankSum=1.067;DB;DP=8;FS=3.332;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.572;POSITIVE_TRAIN_SITE;QD=18.72;ReadPosRankSum=-1.589;SOR=0.105;VQSLOD=1.98;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:2,6:8:54:178,0,54 -chr6 64151771 rs9294215 C G 107.78 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.731;ClippingRankSum=0.731;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.731;POSITIVE_TRAIN_SITE;QD=21.56;ReadPosRankSum=0.731;SOR=1.981;VQSLOD=6.52;culprit=FS GT:AD:DP:GQ:PL 0/1:1,4:5:25:136,0,25 -chr6 64153691 rs2076874 G A 46.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.37;SOR=2.303;VQSLOD=8.47;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:74,6,0 -chr6 64189643 rs58741217 T TCAAA 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.85;SOR=0.693;VQSLOD=7.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 64190067 rs9443931 C A 393.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.203;ClippingRankSum=-0.958;DB;DP=27;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.575;POSITIVE_TRAIN_SITE;QD=14.58;ReadPosRankSum=-1.068;SOR=0.795;VQSLOD=5.07;culprit=FS GT:AD:DP:GQ:PL 0/1:11,14:25:99:422,0,388 -chr6 64190278 rs2622276 A T 386.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.855;ClippingRankSum=-0.153;DB;DP=29;FS=1.455;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.065;POSITIVE_TRAIN_SITE;QD=13.34;ReadPosRankSum=-1.637;SOR=1.112;VQSLOD=2.78;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:14,15:29:99:415,0,464 -chr6 64190446 rs4299811 C T 145.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;ClippingRankSum=0.684;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.322;POSITIVE_TRAIN_SITE;QD=18.22;ReadPosRankSum=0.956;SOR=0.330;VQSLOD=6.88;culprit=FS GT:AD:DP:GQ:PL 0/1:3,5:8:87:174,0,87 -chr6 64190547 rs4557499 G T 91.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;SOR=2.833;VQSLOD=8.49;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:119,9,0 -chr6 64191578 rs10943822 A T 30.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.001;ClippingRankSum=0.248;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.248;POSITIVE_TRAIN_SITE;QD=3.42;ReadPosRankSum=0.248;SOR=0.223;VQSLOD=4.86;culprit=QD GT:AD:DP:GQ:PL 0/1:6,3:9:59:59,0,364 -chr6 64191586 rs10943823 T C 73.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.566;ClippingRankSum=-0.382;DB;DP=11;FS=3.090;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.566;POSITIVE_TRAIN_SITE;QD=6.71;ReadPosRankSum=0.715;SOR=0.132;VQSLOD=1.93;culprit=QD GT:AD:DP:GQ:PL 0/1:8,3:11:99:102,0,417 -chr6 64191949 rs2800052 C T 95.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.76;SOR=2.833;VQSLOD=7.66;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:123,9,0 -chr6 64209875 rs1744139 G A 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.83;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 64209877 rs1779772 T G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.40;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 64221239 rs1744145 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64239405 rs1681942 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64258654 rs1744153 C T 990.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.025;ClippingRankSum=1.004;DB;DP=65;FS=1.109;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=0.846;POSITIVE_TRAIN_SITE;QD=15.24;ReadPosRankSum=1.161;SOR=0.907;VQSLOD=3.16;culprit=FS GT:AD:DP:GQ:PL 0/1:32,33:65:99:1019,0,1066 -chr6 64289938 . AT A 167.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.598;ClippingRankSum=0.045;DP=221;FS=3.210;MLEAC=1;MLEAF=0.500;MQ=56.34;MQ0=0;MQRankSum=0.356;QD=0.76;ReadPosRankSum=-0.923;SOR=0.391;VQSLOD=0.248;culprit=DP GT:AD:DP:GQ:PL 0/1:132,35:167:99:205,0,2502 -chr6 64322622 rs34430878 CT C 638.73 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.494;ClippingRankSum=-0.777;DB;DP=34;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.64;MQ0=0;MQRankSum=1.255;QD=18.79;ReadPosRankSum=1.614;SOR=5.353;VQSLOD=3.84;culprit=FS GT:AD:DP:GQ:PL 1/1:1,28:29:60:676,60,0 -chr6 64322943 rs4583965 C T 56.84 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=12;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.04;MQ0=0;MQRankSum=0.727;QD=4.74;ReadPosRankSum=0.727;SOR=1.609;VQSLOD=3.30;culprit=QD GT:AD:DP:GQ:PL 0/1:1,3:4:18:85,0,18 -chr6 64401952 rs200237690 CATT C 919.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.674;ClippingRankSum=-0.006;DB;DP=77;FS=1.337;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=-2.870;POSITIVE_TRAIN_SITE;QD=11.94;ReadPosRankSum=-0.436;SOR=1.105;VQSLOD=1.29;culprit=MQRankSum GT:AD:DP:GQ:PL 0/1:45,26:71:99:957,0,2148 -chr6 64419024 . CT C 25.74 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.086;ClippingRankSum=-2.457;DP=199;FS=4.601;MLEAC=1;MLEAF=0.500;MQ=57.02;MQ0=0;MQRankSum=0.154;QD=0.13;ReadPosRankSum=-0.940;SOR=0.158 GT:AD:DP:GQ:PL 0/1:142,25:167:63:63,0,2866 -chr6 64472270 rs4710257 A C 1520.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.301;ClippingRankSum=-0.541;DB;DP=75;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.155;POSITIVE_TRAIN_SITE;QD=20.28;ReadPosRankSum=-1.387;SOR=0.569;VQSLOD=4.26;culprit=FS GT:AD:DP:GQ:PL 0/1:32,43:75:99:1549,0,1031 -chr6 64498933 rs147210136 G A 2218.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.180;ClippingRankSum=0.271;DB;DP=150;FS=9.259;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.467;POSITIVE_TRAIN_SITE;QD=14.79;ReadPosRankSum=1.950;SOR=0.286;VQSLOD=0.949;culprit=FS GT:AD:DP:GQ:PL 0/1:75,74:149:99:2247,0,2088 -chr6 64513363 . C A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64523255 . T C 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64574392 rs10638627 C CTT 140.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.729;ClippingRankSum=0.729;DB;DP=11;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.98;MQ0=0;MQRankSum=0.361;POSITIVE_TRAIN_SITE;QD=12.79;ReadPosRankSum=-0.361;SOR=0.892;VQSLOD=6.60;culprit=FS GT:AD:DP:GQ:PL 0/1:4,5:9:99:178,0,138 -chr6 64574396 rs10645485 T TTC 100.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.219;ClippingRankSum=-0.361;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.361;QD=11.19;ReadPosRankSum=-0.361;SOR=0.527;VQSLOD=4.79;culprit=FS GT:AD:DP:GQ:PL 0/1:5,4:9:99:138,0,178 -chr6 64577850 rs321500 A G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64627882 rs677250 T C 63.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=7.65;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 64686503 rs9362331 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64694354 rs4710457 C T 3197.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.855;ClippingRankSum=1.756;DB;DP=194;FS=1.841;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.786;POSITIVE_TRAIN_SITE;QD=16.48;ReadPosRankSum=2.117;SOR=0.546;VQSLOD=2.30;culprit=DP GT:AD:DP:GQ:PL 0/1:92,101:193:99:3226,0,2888 -chr6 64694560 rs1482457 G A 2447.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.451;ClippingRankSum=0.305;DB;DP=164;FS=1.687;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.165;POSITIVE_TRAIN_SITE;QD=14.93;ReadPosRankSum=-0.002;SOR=0.497;VQSLOD=2.46;culprit=DP GT:AD:DP:GQ:PL 0/1:89,74:163:99:2476,0,2876 -chr6 64694620 rs1482456 T C 1132.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=5.667;ClippingRankSum=0.220;DB;DP=67;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.663;POSITIVE_TRAIN_SITE;QD=16.91;ReadPosRankSum=2.755;SOR=1.516;VQSLOD=4.16;culprit=FS GT:AD:DP:GQ:PL 0/1:35,32:67:99:1161,0,1169 -chr6 64708907 rs66502009 A C 2569.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.193;ClippingRankSum=2.479;DB;DP=165;FS=4.658;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.156;POSITIVE_TRAIN_SITE;QD=15.57;ReadPosRankSum=1.406;SOR=1.162;VQSLOD=1.60;culprit=DP GT:AD:DP:GQ:PL 0/1:81,84:165:99:2598,0,2412 -chr6 64752796 rs10944301 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64840987 rs3013170 T C 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=0.693;VQSLOD=7.79;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 64885636 rs4310034 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64949401 rs35507550 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=33.24;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64966049 rs2057165 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64968295 rs2057160 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 64995013 rs6917553 G C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65012918 rs9444712 T C 558.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-4.612;ClippingRankSum=0.176;DB;DP=44;FS=1.724;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.129;POSITIVE_TRAIN_SITE;QD=12.70;ReadPosRankSum=-1.045;SOR=0.412;VQSLOD=2.58;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:22,22:44:99:587,0,721 -chr6 65013122 rs11753319 C G 92.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.368;ClippingRankSum=0.421;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.000;POSITIVE_TRAIN_SITE;QD=11.60;ReadPosRankSum=0.000;SOR=1.609;VQSLOD=6.06;culprit=FS GT:AD:DP:GQ:PL 0/1:4,4:8:99:121,0,142 -chr6 65013202 rs7739082 A C 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.615;ClippingRankSum=-0.168;DB;DP=19;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.168;QD=1.04;ReadPosRankSum=0.056;SOR=0.495 GT:AD:DP:GQ:PL 0/1:16,3:19:48:48,0,530 -chr6 65021076 rs1922968 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65031098 rs1922975 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65037680 rs614395 G C 38.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.956;ClippingRankSum=0.322;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.517;POSITIVE_TRAIN_SITE;QD=4.85;ReadPosRankSum=-0.322;SOR=0.818;VQSLOD=4.08;culprit=QD GT:AD:DP:GQ:PL 0/1:5,3:8:67:67,0,135 -chr6 65051097 . C T 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65073876 rs671938 G T 51.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.87;SOR=2.303;VQSLOD=8.53;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 -chr6 65076921 . A G 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65084617 rs4518475 C T 44.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=14.92;ReadPosRankSum=-0.736;SOR=0.223;VQSLOD=5.99;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:32:73,0,32 -chr6 65168481 rs35441646 C CT 30.71 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.35;SOR=0.693;VQSLOD=8.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0 -chr6 65204065 rs13211837 C G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65210797 rs34848022 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65218097 rs9362916 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65229459 rs13202092 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65236845 rs4710276 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65245271 . G C 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65274426 rs140935331 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65302877 rs75420781 A T 134.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.495;ClippingRankSum=-0.198;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.198;POSITIVE_TRAIN_SITE;QD=19.25;ReadPosRankSum=-1.495;SOR=1.609;VQSLOD=5.71;culprit=FS GT:AD:DP:GQ:PL 0/1:2,5:7:61:163,0,61 -chr6 65302898 rs16895524 A G 263.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.313;ClippingRankSum=1.381;DB;DP=13;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=0;MQRankSum=0.533;POSITIVE_TRAIN_SITE;QD=20.29;ReadPosRankSum=0.817;SOR=1.179;VQSLOD=6.63;culprit=FS GT:AD:DP:GQ:PL 0/1:5,8:13:99:292,0,150 -chr6 65302915 rs11331907 GA G 124.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.088;ClippingRankSum=0.971;DB;DP=18;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=55.86;MQ0=0;MQRankSum=-1.678;POSITIVE_TRAIN_SITE;QD=6.93;ReadPosRankSum=2.208;SOR=0.693;VQSLOD=3.97;culprit=FS GT:AD:DP:GQ:PL 0/1:9,9:18:99:162,0,204 -chr6 65302987 rs139235690 ATATCT A 997.73 VQSRTrancheINDEL99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=2.195;ClippingRankSum=0.287;DB;DP=46;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=47.75;MQ0=0;MQRankSum=-3.550;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=21.69;ReadPosRankSum=3.163;SOR=0.571;VQSLOD=-9.260e-02;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:19,26:45:99:1035,0,709 -chr6 65303044 rs199667034 T G 104.77 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.500;AN=2;BaseQRankSum=-5.183;ClippingRankSum=1.517;DB;DP=59;FS=83.060;MLEAC=1;MLEAF=0.500;MQ=52.39;MQ0=0;MQRankSum=0.300;QD=1.78;ReadPosRankSum=-1.257;SOR=5.992;VQSLOD=-1.136e+01;culprit=FS GT:AD:DP:GQ:PL 0/1:40,19:59:99:133,0,1230 -chr6 65303100 rs17404123 T C 1344.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.901;ClippingRankSum=-0.677;DB;DP=82;FS=0.838;MLEAC=1;MLEAF=0.500;MQ=54.84;MQ0=0;MQRankSum=-1.556;POSITIVE_TRAIN_SITE;QD=16.40;ReadPosRankSum=0.481;SOR=0.826;VQSLOD=2.46;culprit=FS GT:AD:DP:GQ:PL 0/1:36,46:82:99:1373,0,1059 -chr6 65303381 rs17290119 T C 46.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.736;POSITIVE_TRAIN_SITE;QD=15.59;ReadPosRankSum=0.736;SOR=1.179;VQSLOD=6.60;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:31:75,0,31 -chr6 65305972 rs11759796 G A 55.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.87;SOR=0.693;VQSLOD=8.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:83,6,0 -chr6 65318362 rs9445030 C T 61.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.43;SOR=1.179;VQSLOD=8.59;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0 -chr6 65341959 rs3028242 T TATAAC 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=8.22;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 65365989 rs9445092 T C 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=2.303;VQSLOD=9.17;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 65369802 rs148392797 C A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65379468 rs1338822 A T 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=4.02;ReadPosRankSum=-0.736;SOR=0.223 GT:AD:DP:GQ:PL 0/1:1,2:3:32:40,0,32 -chr6 65423976 rs9452511 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65430160 rs9354068 C T 53.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=5.09;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 65447951 rs70999169 A AG 84.25 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.08;SOR=1.179;VQSLOD=8.62;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:121,9,0 -chr6 65473673 rs60268597 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65510460 rs34778588 CT C 514.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.895;ClippingRankSum=-0.724;DB;DP=67;FS=1.771;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=0;MQRankSum=-0.443;QD=7.68;ReadPosRankSum=1.520;SOR=1.167;VQSLOD=0.651;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:28,30:58:99:552,0,543 -chr6 65523111 rs9345532 A C 67.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.684;ClippingRankSum=0.322;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.920;POSITIVE_TRAIN_SITE;QD=8.47;ReadPosRankSum=-0.322;SOR=0.368;VQSLOD=5.25;culprit=QD GT:AD:DP:GQ:PL 0/1:5,3:8:96:96,0,177 -chr6 65525121 rs1390272 C T 133.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.271;ClippingRankSum=0.922;DB;DP=16;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.488;POSITIVE_TRAIN_SITE;QD=8.36;ReadPosRankSum=-1.139;SOR=0.412;VQSLOD=5.72;culprit=QD GT:AD:DP:GQ:PL 0/1:10,6:16:99:162,0,313 -chr6 65533004 rs34714059 A G 223.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.546;ClippingRankSum=-0.296;DB;DP=10;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.546;POSITIVE_TRAIN_SITE;QD=22.38;ReadPosRankSum=-0.296;SOR=1.609;VQSLOD=5.97;culprit=FS GT:AD:DP:GQ:PL 0/1:3,7:10:91:252,0,91 -chr6 65545787 rs2172886 A G 63.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.09;SOR=1.179;VQSLOD=7.94;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:91,9,0 -chr6 65553444 rs2643788 A T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65569554 rs2146756 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65596759 rs7743515 G A 2710.77 PASS AC=2;AF=1.00;AN=2;DB;DP=75;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.69;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.59;SOR=2.895;VQSLOD=5.93;culprit=FS GT:AD:DP:GQ:PL 1/1:0,75:75:99:2739,226,0 -chr6 65611391 rs4710510 T G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65611814 rs57706332 T C 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=2.303;VQSLOD=7.90;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 65611832 rs142709378 A C 128.03 PASS AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.01;SOR=3.258;VQSLOD=6.74;culprit=FS GT:AD:DP:GQ:PL 1/1:0,4:4:12:156,12,0 -chr6 65611952 rs59518422 T TATTA 1930.73 PASS AC=2;AF=1.00;AN=2;DB;DP=44;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.96;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.09;SOR=3.767;VQSLOD=5.99;culprit=FS GT:AD:DP:GQ:PL 1/1:0,43:43:99:1968,132,0 -chr6 65612302 rs75634595 A G 3301.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.382;ClippingRankSum=-0.220;DB;DP=215;FS=1.153;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=0.451;POSITIVE_TRAIN_SITE;QD=15.36;ReadPosRankSum=2.299;SOR=0.598;VQSLOD=1.86;culprit=DP GT:AD:DP:GQ:PL 0/1:108,107:215:99:3330,0,3121 -chr6 65622463 rs9294631 A G 2159.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=4.924;ClippingRankSum=-0.947;DB;DP=134;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=1.365;POSITIVE_TRAIN_SITE;QD=16.12;ReadPosRankSum=2.546;SOR=0.693;VQSLOD=3.14;culprit=FS GT:AD:DP:GQ:PL 0/1:70,64:134:99:2188,0,2257 -chr6 65622662 rs9445437 G C 2121.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=5.294;ClippingRankSum=0.507;DB;DP=143;FS=5.248;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.124;POSITIVE_TRAIN_SITE;QD=14.84;ReadPosRankSum=1.501;SOR=1.441;VQSLOD=1.80;culprit=DP GT:AD:DP:GQ:PL 0/1:81,62:143:99:2150,0,2628 -chr6 65622769 rs74484316 A G 456.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.723;ClippingRankSum=-1.231;DB;DP=21;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.336;POSITIVE_TRAIN_SITE;QD=21.75;ReadPosRankSum=1.007;SOR=1.508;VQSLOD=5.31;culprit=FS GT:AD:DP:GQ:PL 0/1:7,14:21:99:485,0,229 -chr6 65622836 rs41516844 C A 40.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;ClippingRankSum=1.026;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;POSITIVE_TRAIN_SITE;QD=10.19;ReadPosRankSum=-1.026;SOR=0.693;VQSLOD=6.04;culprit=FS GT:AD:DP:GQ:PL 0/1:2,2:4:69:69,0,76 -chr6 65632558 rs6455016 T C 256.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=4.174;VQSLOD=6.56;culprit=FS GT:AD:DP:GQ:PL 1/1:0,7:7:21:285,21,0 -chr6 65678272 rs137904067 C T 28.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.922;ClippingRankSum=-0.922;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.922;QD=4.11;ReadPosRankSum=0.922;SOR=0.223 GT:AD:DP:GQ:PL 0/1:5,2:7:57:57,0,186 -chr6 65715710 . G A 111.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.219;ClippingRankSum=-1.159;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.876;QD=12.42;ReadPosRankSum=-0.361;SOR=0.368;VQSLOD=4.52;culprit=FS GT:AD:DP:GQ:PL 0/1:4,5:9:99:140,0,137 -chr6 65721195 rs7751922 G A 84.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=48.33;MQ0=0;QD=28.09;SOR=2.833;VQSLOD=7.19;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:112,9,0 -chr6 65831684 rs9363336 G A 64.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.43;SOR=1.179;VQSLOD=8.84;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:92,9,0 -chr6 65995024 rs13214404 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 65999709 rs6455035 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66005609 rs34666704 AT A 487.73 PASS AC=2;AF=1.00;AN=2;DB;DP=20;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.39;SOR=6.091;VQSLOD=6.41;culprit=FS GT:AD:DP:GQ:PL 1/1:0,20:20:60:525,60,0 -chr6 66005740 rs35045551 G GA 1585.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.677;ClippingRankSum=-0.710;DB;DP=159;FS=1.564;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=0.316;POSITIVE_TRAIN_SITE;QD=9.97;ReadPosRankSum=1.276;SOR=0.921;VQSLOD=1.90;culprit=DP GT:AD:DP:GQ:PL 0/1:79,74:153:99:1623,0,1557 -chr6 66005857 rs17411795 T A 4088.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.317;ClippingRankSum=-0.640;DB;DP=271;FS=2.014;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=1.167;POSITIVE_TRAIN_SITE;QD=15.09;ReadPosRankSum=2.177;SOR=0.759;VQSLOD=1.94;culprit=DP GT:AD:DP:GQ:PL 0/1:136,134:270:99:4117,0,4192 -chr6 66005888 rs9342464 C T 4205.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=8.627;ClippingRankSum=0.069;DB;DP=251;FS=0.459;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.018;POSITIVE_TRAIN_SITE;QD=16.76;ReadPosRankSum=0.065;SOR=0.647;VQSLOD=1.79;culprit=FS GT:AD:DP:GQ:PL 0/1:126,125:251:99:4234,0,3830 -chr6 66005970 rs9345601 G A 3380.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.543;ClippingRankSum=-0.936;DB;DP=213;FS=2.475;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=-1.449;POSITIVE_TRAIN_SITE;QD=15.87;ReadPosRankSum=1.107;SOR=0.516;VQSLOD=1.23;culprit=DP GT:AD:DP:GQ:PL 0/1:103,109:212:99:3409,0,3103 -chr6 66006148 rs9342465 A C 503.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.574;ClippingRankSum=0.709;DB;DP=21;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.485;POSITIVE_TRAIN_SITE;QD=23.99;ReadPosRankSum=0.485;SOR=1.508;VQSLOD=5.36;culprit=FS GT:AD:DP:GQ:PL 0/1:7,14:21:99:532,0,220 -chr6 66013183 . G A 123.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.273;ClippingRankSum=-0.270;DP=20;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=21.81;MQ0=0;MQRankSum=-0.039;QD=6.19;ReadPosRankSum=0.656;SOR=0.368;VQSLOD=3.44;culprit=QD GT:AD:DP:GQ:PL 0/1:12,8:20:99:152,0,259 -chr6 66014572 rs75369872 A G 25.75 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=22.00;MQ0=0;QD=12.88;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:53,6,0 -chr6 66018514 rs117228350 A C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=46.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66036758 rs13209408 G A 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.23;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 66045077 rs1502965 C T 2159.77 PASS AC=2;AF=1.00;AN=2;DB;DP=61;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.89;SOR=2.584;VQSLOD=6.42;culprit=FS GT:AD:DP:GQ:PL 1/1:0,61:61:99:2188,183,0 -chr6 66045118 rs1502964 T C 1434.77 PASS AC=2;AF=1.00;AN=2;DB;DP=42;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.16;SOR=6.091;VQSLOD=6.20;culprit=FS GT:AD:DP:GQ:PL 1/1:0,42:42:99:1463,126,0 -chr6 66053835 rs1502963 T G 2324.77 PASS AC=2;AF=1.00;AN=2;DB;DP=56;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.46;SOR=6.666;VQSLOD=7.17;culprit=FS GT:AD:DP:GQ:PL 1/1:0,56:56:99:2353,168,0 -chr6 66063513 rs1936439 G A 3064.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-6.245;ClippingRankSum=-0.619;DB;DP=169;FS=3.043;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.296;POSITIVE_TRAIN_SITE;QD=18.13;ReadPosRankSum=1.339;SOR=0.465;VQSLOD=2.08;culprit=DP GT:AD:DP:GQ:PL 0/1:65,104:169:99:3093,0,1991 -chr6 66063766 rs1936440 A C 48.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.736;POSITIVE_TRAIN_SITE;QD=16.26;ReadPosRankSum=-0.736;SOR=1.179;VQSLOD=6.26;culprit=FS GT:AD:DP:GQ:PL 0/1:1,2:3:33:77,0,33 -chr6 66066936 rs9294638 G T 172.90 PASS AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.58;SOR=1.981;VQSLOD=6.69;culprit=FS GT:AD:DP:GQ:PL 1/1:0,5:5:15:201,15,0 -chr6 66067315 rs976727 A C 49.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=0.693;VQSLOD=9.30;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 66080074 rs9342469 G C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66112409 rs974110 A G 2596.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.384;ClippingRankSum=-0.001;DB;DP=191;FS=0.540;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.531;POSITIVE_TRAIN_SITE;QD=13.60;ReadPosRankSum=3.882;SOR=0.763;VQSLOD=1.48;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:102,89:191:99:2625,0,3119 -chr6 66115281 rs34154043 G GAAA 3245.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-5.314;ClippingRankSum=1.320;DB;DP=225;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=0;MQRankSum=0.881;POSITIVE_TRAIN_SITE;QD=14.43;ReadPosRankSum=-2.390;SOR=0.705;VQSLOD=1.12;culprit=FS GT:AD:DP:GQ:PL 0/1:99,90:189:99:3283,0,3862 -chr6 66141229 . T C 20.78 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.39;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:48,6,0 -chr6 66160560 rs9354246 A G 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.68;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 66201364 rs9363379 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66204945 rs12193967 G A 2169.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.754;ClippingRankSum=-0.093;DB;DP=128;FS=4.193;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.577;POSITIVE_TRAIN_SITE;QD=16.95;ReadPosRankSum=1.481;SOR=0.652;VQSLOD=2.12;culprit=DP GT:AD:DP:GQ:PL 0/1:58,70:128:99:2198,0,1773 -chr6 66288101 rs150888347 A AAT 77.25 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.36;MQ0=0;QD=25.75;SOR=1.179;VQSLOD=7.22;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:114,9,0 -chr6 66336763 rs6903740 T C 42.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=21.37;SOR=2.303;VQSLOD=8.26;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 -chr6 66336907 rs71736895 CCTTT C 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.85;SOR=2.303;VQSLOD=5.89;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 66351345 rs6925080 A C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66375671 rs7757773 A T 46.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=15.43;SOR=1.179;VQSLOD=7.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:74,9,0 -chr6 66379893 rs57880191 ACTC A 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=2.303;VQSLOD=8.36;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 66379911 rs9283820 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.76;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 66394859 rs1490125 C A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66409784 rs2812776 A G 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;QD=31.37;SOR=2.303;VQSLOD=6.75;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 66409789 rs2814115 T C 62.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=47.12;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.37;SOR=2.303;VQSLOD=8.59;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 -chr6 66411331 rs1490130 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66417384 rs9294647 G T 52.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.37;SOR=0.693;VQSLOD=8.92;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 -chr6 66418352 rs1490129 T C 233.80 PASS AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.40;SOR=0.941;VQSLOD=6.77;culprit=FS GT:AD:DP:GQ:PL 1/1:0,7:7:21:262,21,0 -chr6 66418415 rs4609011 T C 54.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.37;SOR=0.693;VQSLOD=8.89;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:82,6,0 -chr6 66456318 rs2636129 T C 49.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.87;SOR=2.303;VQSLOD=8.31;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 -chr6 66456442 rs12526256 C T 92.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.76;SOR=1.179;VQSLOD=8.78;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:120,9,0 -chr6 66471880 rs9453396 T G 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66471897 rs9453397 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66471949 rs9445579 C A 53.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.87;SOR=0.693;VQSLOD=8.80;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 66524243 rs2802047 C T 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66546565 rs4388276 G A 48.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=24.37;SOR=2.303;VQSLOD=8.99;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr6 66547178 rs4392709 G A 7412.77 PASS AC=2;AF=1.00;AN=2;DB;DP=208;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.34;MQ0=0;POSITIVE_TRAIN_SITE;QD=35.53;SOR=0.857;VQSLOD=5.34;culprit=QD GT:AD:DP:GQ:PL 1/1:0,208:208:99:7441,625,0 -chr6 66547322 rs9363455 T G 5109.77 PASS AC=2;AF=1.00;AN=2;DB;DP=152;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=0;QD=33.62;SOR=1.319;VQSLOD=4.64;culprit=FS GT:AD:DP:GQ:PL 1/1:0,152:152:99:5138,456,0 -chr6 66568995 rs6931427 G A 62.28 PASS AC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=20.76;SOR=1.179;VQSLOD=8.21;culprit=FS GT:AD:DP:GQ:PL 1/1:0,3:3:9:90,9,0 -chr6 66596125 rs9283821 G A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66610269 rs9363483 A C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66710291 rs1484569 C A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66763069 rs1385225 A G 57.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.87;SOR=0.693;VQSLOD=9.11;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:85,6,0 -chr6 66763131 . T A 21.77 LowQual AC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66802808 rs4710310 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66803535 rs2881644 C A 8655.77 PASS AC=2;AF=1.00;AN=2;DB;DP=238;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.52;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.36;SOR=0.789;VQSLOD=5.13;culprit=FS GT:AD:DP:GQ:PL 1/1:0,237:237:99:8684,713,0 -chr6 66803769 rs55951409 G GGTTTCT 2785.73 PASS AC=2;AF=1.00;AN=2;DB;DP=59;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=31.86;MQ0=0;QD=27.53;SOR=0.960;VQSLOD=4.58;culprit=FS GT:AD:DP:GQ:PL 1/1:0,57:57:99:2823,189,0 -chr6 66804609 rs147166458 GACTC G 322.75 PASS AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=45.87;MQ0=0;POSITIVE_TRAIN_SITE;QD=31.87;SOR=1.179;VQSLOD=5.97;culprit=FS GT:AD:DP:GQ:PL 1/1:0,8:8:24:360,24,0 -chr6 66804622 rs3925325 G C 368.78 PASS AC=2;AF=1.00;AN=2;DB;DP=8;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.49;MQ0=0;QD=30.30;SOR=1.179;VQSLOD=5.58;culprit=FS GT:AD:DP:GQ:PL 1/1:0,8:8:27:397,27,0 -chr6 66804958 rs3030466 C CCT 52.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=65.19;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.35;SOR=2.303;VQSLOD=8.57;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:89,6,0 -chr6 66807446 rs7738469 T C 53.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.87;SOR=2.303;VQSLOD=7.44;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:81,6,0 -chr6 66818604 rs3846808 T C 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66829961 rs11287287 AG A 38.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=19.35;SOR=0.693;VQSLOD=8.71;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 -chr6 66836869 rs13217074 A G 56.74 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.37;SOR=0.693;VQSLOD=7.29;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr6 66849936 rs866452 T A 21.77 LowQual AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.88;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 -chr6 66871532 rs138893096 C CAAAG 53.70 PASS AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=26.85;SOR=0.693;VQSLOD=8.24;culprit=FS GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 diff --git a/scripts/varsome_api_annotate_vcf.py b/scripts/varsome_api_annotate_vcf.py new file mode 100755 index 0000000..4cf5b6e --- /dev/null +++ b/scripts/varsome_api_annotate_vcf.py @@ -0,0 +1,56 @@ +#!/usr/bin/env python3 + +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +import argparse +import sys + +from varsome_api.vcf import VCFAnnotator + +__author__ = 'ckopanos' + + +def annotate_vcf(argv): + parser = argparse.ArgumentParser(description='VCF Annotator command line') + parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=True) + parser.add_argument('-g', help='Reference genome either hg19 or hg38', type=str, metavar='Reference Genome', + required=False, default='hg19') + parser.add_argument('-i', + help='Path to vcf file', + type=str, metavar='Input VCF File', required=True) + parser.add_argument('-o', + help='Path to output vcf file', + type=str, metavar='Output VCF File', required=False) + parser.add_argument('-p', + help='Request parameters e.g. add-all-data=1 expand-pubmed-articles=0', + type=str, metavar='Request Params', required=False, nargs='+') + parser.add_argument('-t', help='Run vcf annotator using x threads', type=int, default=3, required=False, + metavar='Number of threads') + args = parser.parse_args() + api_key = args.k + vcf_file = args.i + output_vcf_file = args.o + ref_genome = args.g + num_threads = args.t + request_parameters = None + if args.p: + request_parameters = {param[0]: param[1] for param in [param.split("=") for param in args.p]} + vcf_annotator = VCFAnnotator(api_key=api_key, ref_genome=ref_genome, get_parameters=request_parameters, + max_threads=num_threads) + vcf_annotator.annotate(vcf_file, output_vcf_file) + + +if __name__ == "__main__": + annotate_vcf(sys.argv[1:]) diff --git a/scripts/varsome_api_run.py b/scripts/varsome_api_run.py new file mode 100755 index 0000000..e8bc0da --- /dev/null +++ b/scripts/varsome_api_run.py @@ -0,0 +1,127 @@ +#!/usr/bin/env python3 + +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +import argparse +import json +import sys +import os + +from varsome_api.client import VarSomeAPIClient + +__author__ = 'ckopanos' + + +def annotate_variant(argv): + parser = argparse.ArgumentParser(description='Sample VarSome API calls') + parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=False) + parser.add_argument('-g', help='Reference genome either hg19 or hg38', type=str, metavar='Reference Genome', + required=False, default='hg19') + parser.add_argument('-q', + help='Query to lookup in the API e.g. chr19:20082943:1:G or in case of batch request ' + 'e.g. chr15-73027478-T-C rs113488022. Don\'t use it together with the -i option', + type=str, metavar='Query', required=False, nargs='+') + parser.add_argument('-p', + help='Request parameters e.g. add-all-data=1 expand-pubmed-articles=0', + type=str, metavar='Request Params', required=False, nargs='+') + parser.add_argument('-i', + help='Path to text file with variants. It should include one variant per line. Don\'t use it ' + 'together with the -q option', + type=str, metavar='Text/CSV File one line per variant', required=False) + parser.add_argument('-o', + help='Path to output file to store variant annotations', + type=str, metavar='Output File with json entries', required=False) + args = parser.parse_args() + api_key = args.k + query = args.q + ref_genome = args.g + input_file = args.i + output_file = args.o + if query and input_file: + sys.stderr.write("Don't specify -i and -q options together. Use only one of them\n") + sys.exit(1) + if not query and not input_file: + sys.stderr.write("Please either specify -i or -q options\n") + sys.exit(1) + if input_file and not os.path.exists(input_file): + sys.stderr.write('File %s does not exist\n' % input_file) + sys.exit(1) + if output_file and os.path.exists(output_file): + sys.stderr.write('File %s already exists\n' % output_file) + sys.exit(1) + request_parameters = None + if args.p: + request_parameters = {param[0]: param[1] for param in [param.split("=") for param in args.p]} + api = VarSomeAPIClient(api_key) + if query: + if len(query) == 1: + result = api.lookup(query[0], params=request_parameters, ref_genome=ref_genome) + else: + if api_key is None: + sys.exit("You need to pass an api key to perform batch requests") + result = api.batch_lookup(query, params=request_parameters, ref_genome=ref_genome) + if output_file: + write_f = open(output_file, 'w') + json.dump(result, write_f, indent=4, sort_keys=True) + else: + sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result") + sys.stdout.write("\n") + sys.exit(0) + with open(input_file) as f: + variants = f.read().splitlines() + if variants: + if len(variants) > 1000: + sys.stdout.write('Too many variants.. Consider using annotate_vcf instead\n') + sys.stdout.flush() + write_f = None + if output_file: + write_f = open(output_file, 'w') + try: + if api_key is None: + sys.stdout.write('Without an API key, variants will be annotated one a time, ' + 'causing a 429 too many requests error after some time\n') + sys.stdout.flush() + results = [] + for variant in variants: + result = api.lookup(variant, params=request_parameters, ref_genome=ref_genome) + if not result: + result = {'error': 'Could not fetch annotations for %s' % variant} + results.append(result) + if write_f is not None: + json.dump(results, write_f, indent=4, sort_keys=True) + else: + sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result") + sys.stdout.write("\n") + else: + result = api.batch_lookup(variants, params=request_parameters, ref_genome=ref_genome) + if write_f is not None: + json.dump(result, write_f, indent=4, sort_keys=True) + else: + sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result") + sys.stdout.write("\n") + except Exception as e: + # several things might occur. This is to broad, but lets not keep open file handles + sys.stderr.write(str(e)) + sys.stderr.write("\n") + if write_f is not None: + write_f.close() + sys.exit(1) + else: + sys.stderr.write('No variants found in file %s\n' % input_file) + sys.exit(1) + + +if __name__ == "__main__": + annotate_variant(sys.argv[1:]) diff --git a/setup.py b/setup.py old mode 100644 new mode 100755 index 5221bd9..c599bc5 --- a/setup.py +++ b/setup.py @@ -1,4 +1,5 @@ -from setuptools import setup +from setuptools import setup, find_packages +import sys from os import path VERSION = (1, 0, '0b1') @@ -6,29 +7,41 @@ __versionstr__ = '.'.join(map(str, VERSION)) here = path.abspath(path.dirname(__file__)) - +installation_requirements = [ + 'requests>=2.0.0, <3.0.0', + 'PyVCF>=0.6.8', + 'jsonmodels>=2.2' +] +if sys.version_info < (3, 4): + installation_requirements.extend(['asyncio', 'unittest2']) setup( - name='variant_api', + name='varsome_api_client', version=__versionstr__, - packages=['variantapi'], - url='https://github.com/saphetor/variant-api-client-python', + packages=find_packages(".", ), + scripts=['scripts/varsome_api_run.py', 'scripts/varsome_api_annotate_vcf.py'], + url='https://github.com/saphetor/varsome-api-client-python', license='Apache License, Version 2.0', - author='Saphetor', + test_suite='nose.collector', + tests_require=['nose'], + include_package_data=True, + package_data= { + '': ['*.vcf', '*.csv'], + }, + author='Saphetor S.A.', author_email='support@saphetor.com', description='A basic python api client implementation for https://api.varsome.com', classifiers=[ 'Development Status :: 4 - Beta', 'Intended Audience :: Developers', + 'Intended Audience :: Science/Research', 'Operating System :: OS Independent', 'License :: OSI Approved :: Apache License', - 'Programming Language :: Python :: 2.7', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.2', 'Programming Language :: Python :: 3.3', 'Programming Language :: Python :: 3.4', 'Programming Language :: Python :: 3.5', + 'Programming Language :: Python :: 3.6', + 'Topic :: Scientific/Engineering :: Bio-Informatics', ], - install_requires=[ - 'requests>=2.0.0, <3.0.0' - ], + install_requires=installation_requirements, + python_requires='>=3.3', ) diff --git a/simpleVCFClient.py b/simpleVCFClient.py deleted file mode 100644 index 6e6408d..0000000 --- a/simpleVCFClient.py +++ /dev/null @@ -1,229 +0,0 @@ -#!/usr/bin/env python3 - -# A simple client application that does the following: -# - Loads a VCF file, -# - For each entry in the file, performs a lookup to the Saphetor Variant API. -# The call can be either in batch mode (the default and more efficient way, -# sending a number of variants at a time), or one by one. -# - Extends the VCF description to include gene information for each entry that -# is retreived from the response received from the API. -# - Saves the result, including the gene information (a comma-separated list of -# gene symbols for each variant) in a new file in the VCF format. -# Note that if a row in the input VCF file contains more than one ALT field -# entries, i.e. corresponds to more than one variants, we'll be storing one -# row per variant in the output VCF file. -# -# It uses the following modules: -# pyVCF (http://pyvcf.readthedocs.io/en/latest/) -# variantapi.client (https://github.com/saphetor/variant-api-client-python) - -import argparse -import json -import logging -import vcf -import re -import sys -from sys import argv -from variantapi.client import VariantAPIClient -from vcf.parser import _Info as VcfInfo, field_counts as vcf_field_counts - -__author__ = 'stephanos-androutsellis' - -# Declare reference genome as a global variable -_ref_genome = 1019 - -# Declare the limit of variants we want to lookup in each batch request -_batch_limit = 3 - - -# A class to store variant lookup data: -# - The record from the input VCF file -# - The variant string -# - The corresponding ALT value (convenient for multi-variant records) -class Variant_lookup_data(object): - vcf_record = None - variant_string = "" - alt_value = "" - - # The class constructor/initializer - def __init__(self,vcf_record,variant_string,alt_value): - self.vcf_record=vcf_record - self.variant_string=variant_string - self.alt_value=alt_value - - -def main(argv): - # Read and parse arguments - infile = '' - outfile = '' - do_batch_lookups = True - input_error = False - - parser = argparse.ArgumentParser(description='Simple VCF Client application') - parser.add_argument('-i', help='Input VCF file', type=str, metavar='Input File', required=True) - parser.add_argument('-o', help='Output VCF file', type=str, metavar='Output File', required=True) - parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=False) - parser.add_argument('-g', help='Reference genome either 1019 (default) or 1038', type=int, - metavar='Reference Genome', required=False, default=1019) - parser.add_argument('-nb', help="Do not do batch requests", action='store_true') - - args = parser.parse_args() - infile = args.i - outfile = args.o - api_key = args.k - ref_genome = args.g if args.g is not None else _ref_genome - do_batch_lookups = not args.nb - - # Open and load vcf file into vfc reader object - print ("Reading input file ", infile) - vcf_reader = vcf.Reader(filename=infile, encoding='utf8') - - # Add a new GENE info field in the metadata description, so that we may store such data for each record - vcf_reader.infos['GENE'] = VcfInfo( 'GENE', ".", 'String', 'Concatenated list of GENE sumbols',"","") - - # Prepare output for writing. - print ("Opening output file ", outfile) - vcf_writer = vcf.Writer(open(outfile, 'w'), vcf_reader, lineterminator='\n') - - # Declare an array of Variant_lookup_data objects to hold data for executing the - # lookups and process its outcome. - variant_lookup_data_array = [] - - # A counter for the total number of rows processed thus far - total_counter = 0 - - # Initialize client connection to API - api = VariantAPIClient(api_key) - if (api is None): - print("Failed to connect to API") - sys.exit() - - print("Start parsing input file") - - # Iterate throught all the records read from the input VCF file - while True: - try: - # Get next record (corresponds to a data row in the file) - vcf_record = next(vcf_reader) - - # A vcf_record (i.e. row in the VCF file) may correspond to more than one variants, if it contains - # more than one ALT values. We generate a Variant_lookup_data record for each variant, - # and add them to the variant_lookup_data_array. - # Note: A reference to the same "vcf_record" object will be stored in each Variant_lookup_data record, - # however the "alt" field will contain a different ALT value. - variant_lookup_data_from_vcf_record(vcf_record, variant_lookup_data_array) - - except StopIteration as e: - # Reached end of input VCF file, no new vcf_record was read - vcf_record = None - - # If we are performing batch lookups... - if (do_batch_lookups): - # Check if we have reached (or slightly crossed) the limit of variants we want for the batch request, or the end of the input file. - # Note: In this implementation we may cross the limit if the last vcf_record read contained more than one variants. This is OK. - if (len(variant_lookup_data_array) >= _batch_limit or vcf_record is None): - # Extract variant strings from array. - variant_string_array = [vld.variant_string for vld in variant_lookup_data_array] - - # Execute batch lookup request - batch_data = api.batch_lookup(variant_string_array, ref_genome=ref_genome, params={ 'add-all-data': 1 }) - - # Process response, variant by variant - batch_counter = 0 - for data in batch_data: - process_single_variant_response_data(variant_lookup_data_array[batch_counter], data, vcf_writer) - batch_counter += 1 - - # Clear array - del variant_lookup_data_array[:] - - if (vcf_record is None): - # Reached the end of the file, finish - break - - # If we are performing individual lookups for each variant (which is not recommended for performance issues), - # execute the lookup and process the outcome - else: - if (vcf_record is not None): - # Execute lookup requests for each element in the array - for vld in variant_lookup_data_array: - data = api.lookup(vld.variant_string, ref_genome=ref_genome) - process_single_variant_response_data(vld, data, vcf_writer) - - # Clear array - del variant_lookup_data_array[:] - else: - # Reached the end of the file, finish - break - - total_counter += 1 - if (total_counter % 1000 == 0): - print ("Read ", total_counter, " rows") - - print ("Finished reading ", total_counter, " rows, exiting") - - - -# Processes a vcf_record from the input VCF file, creates Variant_lookup_data objects for the variants -# in the vcf_record, and appends them to the array variant_lookup_data_array that keeps such objects -# for the current lookup. -# Input: -# vcf_record: The record read from the input VCF file -# variant_lookup_data_array: An array of Variant_lookup_data objects for the current lookup. -# Output: -# None as such, but new elements are appended to the input array variant_lookup_data_array -def variant_lookup_data_from_vcf_record(vcf_record, variant_lookup_data_array): - # Concatenate chromosome, position and reference, separated by ":" characters - variant_chromposref = vcf_record.CHROM + ":" + str(vcf_record.POS) + ":" - if (vcf_record.REF is not None): - variant_chromposref += str(vcf_record.REF) - variant_chromposref += ":" - - # For each ALT element, generate a new string and append to the array - if (vcf_record.ALT is not None): - for alt in vcf_record.ALT: - variant_string = variant_chromposref + str(alt) - variant_lookup_data = Variant_lookup_data(vcf_record,variant_string,alt) - variant_lookup_data_array.append(variant_lookup_data) - else: - variant_lookup_data = Variant_lookup_data(vcf_record,variant_chromposref,vcf_record.ALT) - variant_lookup_data_array.append(variant_lookup_data) - - -# Processes a single variant description vcf_record and writes the resulting new record in the output VCF file -# Input: -# variant_lookup_data: A Variant_lookup_data object corresponding to the variant being queried. -# response_data: The data received from the variant API for this specific record. Note that if the record contained more than one -# elements in the ALT field, and thus corresponded to more than one variants, we query the variant API once for each -# variant. -# vcf_writer: The output VCF file handler object -# Output: -# None -def process_single_variant_response_data(variant_lookup_data, response_data, vcf_writer): - # Try to extract the gene_data information from the response - gene_symbols = set() - if 'refseq_transcripts' in response_data.keys() and response_data['refseq_transcripts']: - for t in response_data['refseq_transcripts'][0]['items']: - if 'gene_symbol' in t and t['gene_symbol']: - gene_symbols.add(t['gene_symbol']) - if 'ensembl_transcripts' in response_data.keys() and response_data['ensembl_transcripts']: - for t in response_data['ensembl_transcripts'][0]['items']: - if 'gene_symbol' in t and t['gene_symbol']: - gene_symbols.add(t['gene_symbol']) - - if gene_symbols: - # Concatenate all gene symbols into a comma-separated string - gene_str = ','.join(gene_symbols) - - # Add gene entry in the INFO field, containing the string. - variant_lookup_data.vcf_record.INFO['GENE'] = gene_str - - # Assign the correct ALT value to the vcf_record for this variant. - variant_lookup_data.vcf_record.ALT = [variant_lookup_data.alt_value] - - # Write the record in the output vcf file. - vcf_writer.write_record(variant_lookup_data.vcf_record) - - -if __name__ == '__main__': - main(argv) diff --git a/variantapi/client.py b/variantapi/client.py deleted file mode 100644 index 3adbc84..0000000 --- a/variantapi/client.py +++ /dev/null @@ -1,123 +0,0 @@ -import logging - -import requests -from requests.exceptions import HTTPError, Timeout, ConnectionError, RequestException - -# Set DEBUG variable to affect certain parameters -_debug = False - - -class VariantApiException(Exception): - ERROR_CODES = { - 400: "Bad request. A parameter you have passed is not valid, or something in your request is wrong", - 401: "Not Authorized: either you need to provide authentication credentials, or the credentials provided aren't" - " valid.", - 403: "Bad Request: your request is invalid, and we'll return an error message that tells you why. This is the " - "status code returned if you've exceeded the rate limit (see below).", - 404: "Not Found: either you're requesting an invalid URI or the resource in question doesn't exist", - 500: "Internal Server Error: we did something wrong.", - 501: "Not implemented.", - 502: "Bad Gateway: returned if VariantAPI is down or being upgraded.", - 503: "Service Unavailable: the VariantAPI servers are up, but are overloaded with requests. Try again later.", - 504: "Gateway Timeout", - } - - def __init__(self, status, response=None): - self.status = status - self.response = response - - def __str__(self): - return "%s (%s)" % ( - self.status, - self.ERROR_CODES.get(self.status, 'Unknown error.') if self.response is None else self.response) - - def __repr__(self): - return "%s(status=%s)" % (self.__class__.__name__, self.status) - - -class VariantAPIClientBase(object): - _api_url = 'https://api.varsome.com' if not _debug else 'https://dev-api.varsome.com' - _accepted_methods = ('GET', 'POST') - - def __init__(self, api_key=None): - self.api_key = api_key - self._headers = {'Accept': 'application/json'} - if self.api_key is not None: - self._headers['Authorization'] = "Token " + self.api_key - self.session = requests.Session() - self.session.headers.update(self._headers) - - def _make_request(self, path, method="GET", params=None, json_data=None): - if method not in self._accepted_methods: - raise VariantApiException('', "Unsupported method %s" % method) - try: - if method == "GET": - r = self.session.get(self._api_url + path, params=params) - if method == "POST": - r = self.session.post(self._api_url + path, params=params, json=json_data, - headers={'Content-Type': 'application/json'} if json_data is not None else None) - logging.debug('Time between request and response %s' % r.elapsed) - logging.debug('Content length %s' % len(r.content)) - if r.status_code in VariantApiException.ERROR_CODES: - raise VariantApiException( - r.status_code, - r.json()['detail'] - if r.headers['Content-Type'] == "application/json" else None) - return r - except HTTPError as e: - raise VariantApiException('', "Unknown http error %s" % e) - except Timeout as e: - raise VariantApiException('', "Request timed out %s" % e) - except ConnectionError as e: - raise VariantApiException('', "Connection failure or connection refused %s" % e) - except RequestException as e: - raise VariantApiException('', "Unknown error %s" % e.response) - - def get(self, path, params=None): - response = self._make_request(path, "GET", params=params) - return response.json() - - def post(self, path, params=None, json_data=None): - response = self._make_request(path, "POST", params=params, json_data=json_data) - return response.json() - - -class VariantAPIClient(VariantAPIClientBase): - schema_lookup_path = "/lookup/schema/" - lookup_path = "/lookup/%s/%s" - batch_lookup_path = "/lookup/batch/%s" - - def __init__(self, api_key=None, max_variants_per_batch=200): - super(VariantAPIClient, self).__init__(api_key) - self.max_variants_per_batch = max_variants_per_batch - - def schema(self): - return self.get(self.schema_lookup_path) - - def lookup(self, query, params=None, ref_genome='hg19'): - """ - - :param query: variant representation - :param params: dictionary of key value pairs for http GET parameters. Refer to the api documentation - of https://api.varsome.com for examples - :param ref_genome: reference genome (hg19 or hg38) - :return:dictionary of annotations. refer to https://api.varsome.com/lookup/schema for dictionary properties - """ - return self.get(self.lookup_path % (query, ref_genome), params=params) - - def batch_lookup(self, variants, params=None, ref_genome='hg19'): - """ - - :param variants: list of variant representations - :param params: dictionary of key value pairs for http GET parameters. Refer to the api documentation - of https://api.varsome.com for examples - :param ref_genome: reference genome (hg19 or hg38) - :return: list of dictionaries with annotations per variant refer to https://api.varsome.com/lookup/schema - for dictionary properties - """ - results = [] - for queries in [variants[x:x + self.max_variants_per_batch] for x in range(0, len(variants), - self.max_variants_per_batch)]: - data = self.post(self.batch_lookup_path % ref_genome, params=params, json_data={'variants': queries}) - results.extend(data) - return results diff --git a/variantapi/__init__.py b/varsome_api/__init__.py old mode 100644 new mode 100755 similarity index 100% rename from variantapi/__init__.py rename to varsome_api/__init__.py diff --git a/varsome_api/client.py b/varsome_api/client.py new file mode 100755 index 0000000..2789546 --- /dev/null +++ b/varsome_api/client.py @@ -0,0 +1,193 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +import logging +import asyncio +import concurrent.futures +import re +import os +import requests +from requests.exceptions import HTTPError, Timeout, ConnectionError, RequestException + + +class VarSomeAPIException(Exception): + ERROR_CODES = { + 400: "Bad request. A parameter you have passed is not valid, or something in your request is wrong", + 401: "Not Authorized: either you need to provide authentication credentials, or the credentials provided aren't" + " valid.", + 403: "Bad Request: your request is invalid, and we'll return an error message that tells you why. This is the " + "status code returned if you've exceeded the rate limit (see below).", + 404: "Not Found: either you're requesting an invalid URI or the resource in question doesn't exist", + 500: "Internal Server Error: we did something wrong.", + 501: "Not implemented.", + 502: "Bad Gateway: returned if VariantAPI is down or being upgraded.", + 503: "Service Unavailable: the VariantAPI servers are up, but are overloaded with requests. Try again later.", + 504: "Gateway Timeout", + } + + def __init__(self, status, response=None): + self.status = status + self.response = response + + def __str__(self): + return "%s (%s)" % ( + self.status, + self.ERROR_CODES.get(self.status, 'Unknown error.') if self.response is None else self.response) + + def __repr__(self): + return "%s(status=%s)" % (self.__class__.__name__, self.status) + + +class VarSomeAPIClientBase(object): + _api_url = 'https://api.varsome.com' + _accepted_methods = ('GET', 'POST') + + def __init__(self, api_key=None, logger=None): + if logger is None: + BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) + logger = logging.getLogger(__name__) + logger.setLevel(logging.DEBUG) + formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s') + ch = logging.StreamHandler() + ch.setLevel(logging.DEBUG) + ch.setFormatter(formatter) + logger.addHandler(ch) + self.logger = logger + self.api_key = api_key + self._headers = {'Accept': 'application/json', 'user-agent': 'VarSomeApiClientPython/2.0'} + if self.api_key is not None: + self._headers['Authorization'] = "Token " + self.api_key + self.session = requests.Session() + self.session.headers.update(self._headers) + + def _make_request(self, path, method="GET", params=None, json_data=None): + if method not in self._accepted_methods: + raise VarSomeAPIException('', "Unsupported method %s" % method) + try: + if method == "GET": + r = self.session.get(self._api_url + path, params=params, stream=True) + if method == "POST": + if json_data is None: + raise RuntimeError("You need to provide a post request body") + r = self.session.post(self._api_url + path, params=params, json=json_data, + headers={'Content-Type': 'application/json'}, stream=True) + self.logger.info('Time between request and response %s' % r.elapsed) + self.logger.info('Content length %s' % len(r.content)) + r.raise_for_status() + return r + except HTTPError as e: + response = e.response + if response.status_code in VarSomeAPIException.ERROR_CODES: + error_message = "Unexpected error" + if r.headers['Content-Type'] == "application/json": + error_message = response.json().get("detail", None) + raise VarSomeAPIException(response.status_code, error_message) + raise VarSomeAPIException('', "Unknown http error %s" % e) + except Timeout as e: + raise VarSomeAPIException('', "Request timed out %s" % e) + except ConnectionError as e: + raise VarSomeAPIException('', "Connection failure or connection refused %s" % e) + except RequestException as e: + raise VarSomeAPIException('', "Unknown error %s" % e) + + def get(self, path, params=None): + response = self._make_request(path, "GET", params=params) + return response.json() + + def post(self, path, params=None, json_data=None, raise_exceptions=True): + # handle api errors in batch requests. + try: + response = self._make_request(path, "POST", params=params, json_data=json_data) + return response.json() + except VarSomeAPIException as e: + if raise_exceptions: + raise e + self.logger.error(e) + return {'error': str(e)} + + +class VarSomeAPIClient(VarSomeAPIClientBase): + schema_lookup_path = "/lookup/schema" + lookup_path = "/lookup/%s" + ref_genome_lookup_path = lookup_path + "/%s" + batch_lookup_path = "/lookup/batch/%s" + + def __init__(self, api_key=None, max_variants_per_batch=200): + super(VarSomeAPIClient, self).__init__(api_key) + self.max_variants_per_batch = max_variants_per_batch + + + def query_is_variant_id(self, query): + """ + Query may be a variat identifier developed by Saphetor + :param query: + :return: + """ + return re.search(r'^\d{20}$', str(query)) + + def schema(self): + return self.get(self.schema_lookup_path) + + def lookup(self, query, params=None, ref_genome=None): + """ + + :param query: variant representation + :param params: dictionary of key value pairs for http GET parameters. Refer to the api documentation + of https://api.varsome.com for examples + :param ref_genome: reference genome (hg19 or hg38 or None) default for requests with no ref genome is hg19 + :return:dictionary of annotations. refer to https://api.varsome.com/lookup/schema for dictionary properties + """ + url = self.lookup_path % query + if ref_genome is not None and not self.query_is_variant_id(query): + url = self.ref_genome_lookup_path % (query, ref_genome) + return self.get(url, params=params) + + def batch_lookup(self, variants, params=None, ref_genome='hg19', max_threads=3, raise_exceptions=False): + """ + + :param variants: list of variant representations + :param params: dictionary of key value pairs for http GET parameters. Refer to the api documentation + of https://api.varsome.com for examples + :param ref_genome: reference genome (hg19 or hg38) + :param max_threads: how many concurrent requests to make + (max_variants_per_batch has to be less than len(variants) param to have any effect) + :raise_exceptions: If a post request should raise an exception True, thus terminating the whole process or if it + should proceed to let the process continue + :return: list of dictionaries with annotations per variant refer to https://api.varsome.com/lookup/schema + for dictionary properties + """ + results = [] + + @asyncio.coroutine + def batch(executor): + loop = asyncio.get_event_loop() + futures = [ + loop.run_in_executor( + executor, + self.post, + self.batch_lookup_path % ref_genome, params, {'variants': queries}, raise_exceptions + ) + for queries in [variants[x:x + self.max_variants_per_batch] for x in range(0, len(variants), + self.max_variants_per_batch)] + ] + responses = yield from asyncio.gather(*futures) + for response in responses: + results.extend(response) + # Create a limited thread pool. + executor = concurrent.futures.ThreadPoolExecutor( + max_workers=max_threads, + ) + loop = asyncio.get_event_loop() + loop.run_until_complete(batch(executor)) + return results diff --git a/varsome_api/models/__init__.py b/varsome_api/models/__init__.py new file mode 100755 index 0000000..ee2f4d4 --- /dev/null +++ b/varsome_api/models/__init__.py @@ -0,0 +1,3 @@ +__author__ = "ckopanos" + + diff --git a/varsome_api/models/elements/__init__.py b/varsome_api/models/elements/__init__.py new file mode 100755 index 0000000..276d4c7 --- /dev/null +++ b/varsome_api/models/elements/__init__.py @@ -0,0 +1,17 @@ +__author__ = "ckopanos" + +from .transcript import * +from .broad import * +from .gnomad import * +from .thousand_genomes import * +from .gerp import * +from .isb import * +from .dbnsfp import * +from .dann import * +from .ncbi import * +from .sanger import * +from .icgc import * +from .iarc import * +from .uniprot import * +from .wustl import * +from .gwas import * diff --git a/varsome_api/models/elements/broad.py b/varsome_api/models/elements/broad.py new file mode 100755 index 0000000..6c994f9 --- /dev/null +++ b/varsome_api/models/elements/broad.py @@ -0,0 +1,78 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from jsonmodels import models, fields + +__author__ = "ckopanos" + + +class ExAC(models.Base): + version = fields.StringField(help_text="Version") + ac = fields.IntField(help_text="Allele Count", required=False, nullable=True) + an = fields.IntField(help_text="Allele Number", required=False, nullable=True) + ac_adj = fields.FloatField(help_text="Allele Count", required=False, nullable=True) + an_adj = fields.FloatField(help_text="Allele Number", required=False, nullable=True) + af = fields.FloatField(help_text="Allele Frequency", required=False, nullable=True) + ac_afr = fields.IntField(help_text="Allele Count African", required=False, nullable=True) + ac_amr = fields.IntField(help_text="Allele Count American", required=False, nullable=True) + ac_asj = fields.IntField(help_text="Allele Count Ashkenazi Jewish", required=False, nullable=True) + ac_eas = fields.IntField(help_text="Allele Count East Asian", required=False, nullable=True) + ac_fin = fields.IntField(help_text="Allele Count European (Finnish)", required=False, nullable=True) + ac_nfe = fields.IntField(help_text="Allele Count European (Non-Finnish)", required=False, nullable=True) + ac_oth = fields.IntField(help_text="Allele Count Other", required=False, nullable=True) + ac_sas = fields.IntField(help_text="Allele Count South Asian", required=False, nullable=True) + ac_male = fields.IntField(help_text="Allele Count Male", required=False, nullable=True) + ac_female = fields.IntField(help_text="Allele Count Female", required=False, nullable=True) + hom = fields.IntField(help_text="Number of Homozygotes", required=False, nullable=True) + hemi = fields.IntField(help_text="Number of Hemizygotes", required=False, nullable=True) + ac_hom = fields.FloatField(help_text="Number of Homozygotes", required=False, nullable=True) + ac_hemi = fields.FloatField(help_text="Number of Hemizygotes", required=False, nullable=True) + an_afr = fields.IntField(help_text="Allele Number African", required=False, nullable=True) + an_amr = fields.IntField(help_text="Allele Number American", required=False, nullable=True) + an_asj = fields.IntField(help_text="Allele Number Ashkenazi Jewish", required=False, nullable=True) + an_eas = fields.IntField(help_text="Allele Number East Asian", required=False, nullable=True) + an_fin = fields.IntField(help_text="Allele Number European (Finnish)", required=False, nullable=True) + an_nfe = fields.IntField(help_text="Allele Number European (Non-Finnish)", required=False, nullable=True) + an_oth = fields.IntField(help_text="Allele Number Other", required=False, nullable=True) + an_sas = fields.IntField(help_text="Allele Number South Asian", required=False, nullable=True) + an_male = fields.IntField(help_text="Allele Number Male", required=False, nullable=True) + an_female = fields.IntField(help_text="Allele Number Female", required=False, nullable=True) + hom_afr = fields.IntField(help_text="Number of Homozygotes African", required=False, nullable=True) + hom_amr = fields.IntField(help_text="Number of Homozygotes American", required=False, nullable=True) + hom_asj = fields.IntField(help_text="Number of Homozygotes Ashkenazi Jewish", required=False, nullable=True) + hom_eas = fields.IntField(help_text="Number of Homozygotes East Asian", required=False, nullable=True) + hom_fin = fields.IntField(help_text="Number of Homozygotes European (Finnish)", required=False, nullable=True) + hom_nfe = fields.IntField(help_text="Number of Homozygotes European (Non-Finnish)", required=False, nullable=True) + hom_oth = fields.IntField(help_text="Number of Homozygotes Other", required=False, nullable=True) + hom_sas = fields.IntField(help_text="Number of Homozygotes South Asian", required=False, nullable=True) + hom_male = fields.IntField(help_text="Number of Homozygotes Male", required=False, nullable=True) + hom_female = fields.IntField(help_text="Number of Homozygotes Female", required=False, nullable=True) + hemi_afr = fields.IntField(help_text="Number of Hemizygotes African", required=False, nullable=True) + hemi_amr = fields.IntField(help_text="Number of Hemizygotes American", required=False, nullable=True) + hemi_asj = fields.IntField(help_text="Number of Hemizygotes Ashkenazi Jewish", required=False, nullable=True) + hemi_eas = fields.IntField(help_text="Number of Hemizygotes East Asian", required=False, nullable=True) + hemi_fin = fields.IntField(help_text="Number of Hemizygotes European (Finnish)", required=False, nullable=True) + hemi_nfe = fields.IntField(help_text="Number of Hemizygotes European (Non-Finnish)", required=False, nullable=True) + hemi_oth = fields.IntField(help_text="Number of Hemizygotes Other", required=False, nullable=True) + hemi_sas = fields.IntField(help_text="Number of Hemizygotes South Asian", required=False, nullable=True) + af_afr = fields.FloatField(help_text="Allele Frequency African", required=False, nullable=True) + af_amr = fields.FloatField(help_text="Allele Frequency American", required=False, nullable=True) + af_asj = fields.FloatField(help_text="Allele Frequency Ashkenazi Jewish", required=False, nullable=True) + af_eas = fields.FloatField(help_text="Allele Frequency East Asian", required=False, nullable=True) + af_fin = fields.FloatField(help_text="Allele Frequency European (Finnish)", required=False, nullable=True) + af_nfe = fields.FloatField(help_text="Allele Frequency European (Non-Finnish)", required=False, nullable=True) + af_oth = fields.FloatField(help_text="Allele Frequency Other", required=False, nullable=True) + af_sas = fields.FloatField(help_text="Allele Frequency South Asian", required=False, nullable=True) + af_male = fields.FloatField(help_text="Allele Frequency Male", required=False, nullable=True) + af_female = fields.FloatField(help_text="Allele Frequency Female", required=False, nullable=True) \ No newline at end of file diff --git a/varsome_api/models/elements/dann.py b/varsome_api/models/elements/dann.py new file mode 100755 index 0000000..30d7a73 --- /dev/null +++ b/varsome_api/models/elements/dann.py @@ -0,0 +1,22 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from jsonmodels import models, fields + +__author__ = "ckopanos" + + +class DannSNVs(models.Base): + version = fields.StringField(help_text="Version") + dann_score = fields.FloatField(help_text="DANN Score", required=False, nullable=True) diff --git a/varsome_api/models/elements/dbnsfp.py b/varsome_api/models/elements/dbnsfp.py new file mode 100755 index 0000000..b652327 --- /dev/null +++ b/varsome_api/models/elements/dbnsfp.py @@ -0,0 +1,124 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from jsonmodels import models, fields + +__author__ = "ckopanos" + + +class DbNSFP(models.Base): + version = fields.StringField(help_text="Version") + mutationtaster_pred = fields.ListField(items_types=(str,), help_text="MutationTaster Prediction", + required=False) + mutationtaster_score = fields.ListField(items_types=(float,), + help_text="MutationTaster Accuracy", required=False, nullable=True) + sift_score = fields.ListField(items_types=(float,), help_text="SIFT score", required=False, nullable=True) + sift_prediction = fields.StringField(help_text="SIFT prediction", required=False, nullable=True) + phylop100way_vertebrate = fields.ListField(items_types=(float,), help_text="phyloP100way vertebrate", + required=False) + phylop46way_placental = fields.ListField(items_types=(float,), help_text="phyloP46way placental", + required=False) + phylop46way_primate = fields.ListField(items_types=(float,), help_text="phyloP46way primate", + required=False) + mutationtaster_converted_rankscore = fields.ListField(items_types=(float,), + help_text="MutationTaster converted rankscore", + required=False, nullable=True) + mutationassessor_pred = fields.ListField(items_types=(str,), + help_text="MutationAssessor prediction", + required=False) + mutationassessor_score = fields.ListField(items_types=(float,), help_text="MutationAssessor score", + required=False) + mutationassessor_score_rankscore = fields.ListField(items_types=(float,), + help_text="MutationAssessor rankscore", required=False, + nullable=True) + fathmm_mkl_coding_pred = fields.ListField(items_types=(str,), + help_text="FATHMM-MKL coding prediction", required=False, nullable=True) + fathmm_mkl_coding_score = fields.ListField(items_types=(float,), help_text="FATHMM-MKL coding score", + required=False) + fathmm_mkl_coding_rankscore = fields.ListField(items_types=(float,), + help_text="FATHMM-MKL coding rankscore", required=False, + nullable=True) + fathmm_pred = fields.ListField(items_types=(str,), help_text="FATHMM prediction", required=False, nullable=True) + fathmm_score = fields.ListField(items_types=(float,), help_text="FATHMM score", + required=False) + fathmm_converted_rankscore = fields.ListField(items_types=(float,), help_text="FATHMM converted rankscore", + required=False, nullable=True) + sift_converted_rankscore = fields.ListField(items_types=(float,), help_text="SIFT converted rankscore", + required=False) + metasvm_pred = fields.ListField(items_types=(str,), help_text="MetaSVM prediction", + required=False) + metasvm_score = fields.ListField(items_types=(float,), help_text="MetaSVM score", required=False, nullable=True) + metasvm_rankscore = fields.ListField(items_types=(float,), help_text="MetaSVM rankscore", + required=False) + metalr_pred = fields.ListField(items_types=(str,), help_text="MetalR prediction", required=False, nullable=True) + metalr_score = fields.ListField(items_types=(float,), help_text="MetalR score", required=False, nullable=True) + metalr_rankscore = fields.ListField(items_types=(float,), help_text="MetalR rankscore", required=False, + nullable=True) + provean_pred = fields.ListField(items_types=(str,), help_text="Provean prediction", + required=False) + provean_score = fields.ListField(items_types=(float,), help_text="Provean score", + required=False) + provean_converted_rankscore = fields.ListField(items_types=(float,), + help_text="Provean converted rankscore", required=False, + nullable=True) + lrt_pred = fields.ListField(items_types=(str,), help_text="LRT prediction", required=False, nullable=True) + lrt_score = fields.ListField(items_types=(float,), help_text="LRT score", required=False, nullable=True) + lrt_converted_rankscore = fields.ListField(items_types=(float,), help_text="LRT converted rankscore", + required=False) + lrt_omega = fields.ListField(items_types=(float,), help_text="LRT Omega", required=False, nullable=True) + cadd_raw = fields.ListField(items_types=(float,), help_text="CADD raw score", required=False, nullable=True) + cadd_raw_rankscore = fields.ListField(items_types=(float,), help_text="CADD raw rankscore", + required=False) + cadd_phred = fields.ListField(items_types=(float,), help_text="CADD phred", required=False, nullable=True) + gm12878_confidence_value = fields.ListField(items_types=(float,), + help_text="GM12878 fitCons confidence value", required=False, + nullable=True) + gm12878_fitcons_score = fields.ListField(items_types=(float,), help_text="GM12878 fitCons score", + required=False) + gm12878_fitcons_score_rankscore = fields.ListField(items_types=(float,), + help_text="GM12878 fitCons rankscore", required=False, + nullable=True) + siphy_29way_logodds_rankscore = fields.ListField(items_types=(float,), + help_text="SiPhy29way logOdds rankscore", required=False, + nullable=True) + siphy_29way_pi = fields.ListField(items_types=(float,), + help_text="SiPhy29way pi", required=False, nullable=True) + phylop20way_mammalian = fields.ListField(items_types=(float,), help_text="phyloP20way mammalian", + required=False) + phylop20way_mammalian_rankscore = fields.ListField(items_types=(float,), + help_text="phyloP20way mammalian rankscore", required=False, + nullable=True) + phylop100way_vertebrate_rankscore = fields.ListField(items_types=(float,), + help_text="phyloP100way vertebrate rankscore", required=False, + nullable=True) + phastcons20way_mammalian = fields.ListField(items_types=(float,), help_text="phastCons20way mammalian", + required=False) + phastcons20way_mammalian_rankscore = fields.ListField(items_types=(float,), + help_text="phastCons20way mammalian rankscore", + required=False, nullable=True) + phastcons100way_vertebrate = fields.ListField(items_types=(float,), + help_text="phastCons100way vertebrate", required=False, nullable=True) + phastcons100way_vertebrate_rankscore = fields.ListField(items_types=(float,), + help_text="phastCons100way vertebrate rankscore", + required=False, nullable=True) + vest3_score = fields.ListField(items_types=(float,), help_text="VEST3 score", + required=False) + vest3_rankscore = fields.ListField(items_types=(float,), + help_text="VEST3 rankscore", required=False, nullable=True) + + +class DBscSNV(models.Base): + version = fields.StringField(help_text="Version") + ada_score = fields.ListField(items_types=(float, ), help_text='ADA Score', required=False, nullable=True) + rf_score = fields.ListField(items_types=(float,), help_text='RF Score', required=False, nullable=True) \ No newline at end of file diff --git a/varsome_api/models/elements/gerp.py b/varsome_api/models/elements/gerp.py new file mode 100755 index 0000000..06b34b3 --- /dev/null +++ b/varsome_api/models/elements/gerp.py @@ -0,0 +1,23 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from jsonmodels import models, fields + +__author__ = "ckopanos" + + +class Gerp(models.Base): + version = fields.StringField(help_text="Version") + gerp_nr = fields.ListField(items_types=(float, type(None)), required=False, help_text="GERP NR", nullable=True) + gerp_rs = fields.ListField(items_types=(float, type(None)), required=False, help_text="GERP RS", nullable=True) diff --git a/varsome_api/models/elements/gnomad.py b/varsome_api/models/elements/gnomad.py new file mode 100755 index 0000000..4baf52d --- /dev/null +++ b/varsome_api/models/elements/gnomad.py @@ -0,0 +1,78 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from jsonmodels import models, fields + +__author__ = "ckopanos" + + +class GnomADCoverage(models.Base): + version = fields.StringField(help_text="Version") + coverage_mean = fields.ListField(help_text="Mean coverage", + items_types=(float, type(None)), required=False, nullable=True) + coverage_median = fields.ListField(help_text="Median coverage", + items_types=(float, type(None)), required=False, nullable=True) + coverage_20_frequency = fields.ListField(help_text="Proportion of samples with over 20x", + items_types=(float, type(None)), + required=False, nullable=True) + + +class GnomAD(models.Base): + version = fields.StringField(help_text="Version") + ac = fields.IntField(help_text="Allele Count", required=False, nullable=True) + an = fields.IntField(help_text="Allele Number", required=False, nullable=True) + ac_adj = fields.FloatField(help_text="Allele Count", required=False, nullable=True) + an_adj = fields.FloatField(help_text="Allele Number", required=False, nullable=True) + af = fields.FloatField(help_text="Allele Frequency", required=False, nullable=True) + ac_afr = fields.IntField(help_text="Allele Count African", required=False, nullable=True) + ac_amr = fields.IntField(help_text="Allele Count American", required=False, nullable=True) + ac_asj = fields.IntField(help_text="Allele Count Ashkenazi Jewish", required=False, nullable=True) + ac_eas = fields.IntField(help_text="Allele Count East Asian", required=False, nullable=True) + ac_fin = fields.IntField(help_text="Allele Count European (Finnish)", required=False, nullable=True) + ac_nfe = fields.IntField(help_text="Allele Count European (Non-Finnish)", required=False, nullable=True) + ac_oth = fields.IntField(help_text="Allele Count Other", required=False, nullable=True) + ac_male = fields.IntField(help_text="Allele Count Male", required=False, nullable=True) + ac_female = fields.IntField(help_text="Allele Count Female", required=False, nullable=True) + hom = fields.IntField(help_text="Number of Homozygotes", required=False, nullable=True) + hemi = fields.IntField(help_text="Number of Hemizygotes", required=False, nullable=True) + ac_hom = fields.FloatField(help_text="Number of Homozygotes", required=False, nullable=True) + ac_hemi = fields.FloatField(help_text="Number of Hemizygotes", required=False, nullable=True) + an_afr = fields.IntField(help_text="Allele Number African", required=False, nullable=True) + an_amr = fields.IntField(help_text="Allele Number American", required=False, nullable=True) + an_asj = fields.IntField(help_text="Allele Number Ashkenazi Jewish", required=False, nullable=True) + an_eas = fields.IntField(help_text="Allele Number East Asian", required=False, nullable=True) + an_fin = fields.IntField(help_text="Allele Number European (Finnish)", required=False, nullable=True) + an_nfe = fields.IntField(help_text="Allele Number European (Non-Finnish)", required=False, nullable=True) + an_oth = fields.IntField(help_text="Allele Number Other", required=False, nullable=True) + an_male = fields.IntField(help_text="Allele Number Male", required=False, nullable=True) + an_female = fields.IntField(help_text="Allele Number Female", required=False, nullable=True) + hom_afr = fields.IntField(help_text="Number of Homozygotes African", required=False, nullable=True) + hom_amr = fields.IntField(help_text="Number of Homozygotes American", required=False, nullable=True) + hom_asj = fields.IntField(help_text="Number of Homozygotes Ashkenazi Jewish", required=False, nullable=True) + hom_eas = fields.IntField(help_text="Number of Homozygotes East Asian", required=False, nullable=True) + hom_fin = fields.IntField(help_text="Number of Homozygotes European (Finnish)", required=False, nullable=True) + hom_nfe = fields.IntField(help_text="Number of Homozygotes European (Non-Finnish)", required=False, nullable=True) + hom_oth = fields.IntField(help_text="Number of Homozygotes Other", required=False, nullable=True) + hom_male = fields.IntField(help_text="Number of Homozygotes Male", required=False, nullable=True) + hom_female = fields.IntField(help_text="Number of Homozygotes Female", required=False, nullable=True) + af_afr = fields.FloatField(help_text="Allele Frequency African", required=False, nullable=True) + af_amr = fields.FloatField(help_text="Allele Frequency American", required=False, nullable=True) + af_asj = fields.FloatField(help_text="Allele Frequency Ashkenazi Jewish", required=False, nullable=True) + af_eas = fields.FloatField(help_text="Allele Frequency East Asian", required=False, nullable=True) + af_fin = fields.FloatField(help_text="Allele Frequency European (Finnish)", required=False, nullable=True) + af_nfe = fields.FloatField(help_text="Allele Frequency European (Non-Finnish)", required=False, nullable=True) + af_oth = fields.FloatField(help_text="Allele Frequency Other", required=False, nullable=True) + af_male = fields.FloatField(help_text="Allele Frequency Male", required=False, nullable=True) + af_female = fields.FloatField(help_text="Allele Frequency Female", required=False, nullable=True) + main_data = fields.StringField(help_text="Main data point", required=False, nullable=True) diff --git a/varsome_api/models/elements/gwas.py b/varsome_api/models/elements/gwas.py new file mode 100755 index 0000000..f339728 --- /dev/null +++ b/varsome_api/models/elements/gwas.py @@ -0,0 +1,42 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from jsonmodels import models, fields + +__author__ = "ckopanos" + + +class GWASDetails(models.Base): + gwas_symbol = fields.StringField(help_text="GWAS symbol", required=False, nullable=True) + date = fields.StringField(help_text="Date", required=False, nullable=True) + study = fields.StringField(help_text="Study", required=False, nullable=True) + disease_or_trait = fields.StringField(help_text="Disease or trait", required=False, nullable=True) + mapped_traits = fields.ListField(items_types=(str,), help_text="Mapped trait", required=False, nullable=True) + mapped_trait_urls = fields.ListField(items_types=(str,), help_text="Mapped trait URL", required=False, + nullable=True) + strongest_snp_risk_allele = fields.StringField(help_text="Strongest SNP risk allele", required=False, nullable=True) + odds_ratio = fields.FloatField(help_text="Odds ratio", required=False, nullable=True) + p_value = fields.StringField(help_text="p value", required=False, nullable=True) + confidence_range_95_low = fields.FloatField(help_text="Confidence range 95% low", required=False, nullable=True) + confidence_range_95_high = fields.FloatField(help_text="Confidence range 95% high", required=False, nullable=True) + confidence_comment = fields.StringField(help_text="Confidence comment", required=False, nullable=True) + initial_sample_size = fields.StringField(help_text="Initial sample size", required=False, nullable=True) + replication_sample_size = fields.StringField(help_text="Replication sample size", required=False, nullable=True) + pub_med_references = fields.ListField(items_types=(int,), help_text="PubMed References", required=False, + nullable=True) + + +class GWAS(models.Base): + version = fields.StringField(help_text="Version") + items = fields.ListField(help_text='Details', items_types=(GWASDetails,)) diff --git a/varsome_api/models/elements/iarc.py b/varsome_api/models/elements/iarc.py new file mode 100755 index 0000000..a3db37f --- /dev/null +++ b/varsome_api/models/elements/iarc.py @@ -0,0 +1,56 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + + +from jsonmodels import models, fields + +__author__ = "ckopanos" + + +class TP53GermlineDetails(models.Base): + age_at_diagnosis = fields.IntField(help_text="Age at diagnosis", required=False, nullable=True) + country = fields.StringField(help_text="Country", required=False, nullable=True) + effect = fields.StringField(help_text="Effect", required=False, nullable=True) + familycase = fields.StringField(help_text="Family case", required=False, nullable=True) + familycase_group = fields.StringField(help_text="Family case group", required=False, nullable=True) + family_code = fields.StringField(help_text="Family code", required=False, nullable=True) + generation = fields.StringField(help_text="Generation", required=False, nullable=True) + morphology = fields.StringField(help_text="Morphology", required=False, nullable=True) + sex = fields.StringField(help_text="Sex", required=False, nullable=True) + topography = fields.StringField(help_text="Topography", required=False, nullable=True) + unaffected = fields.IntField(help_text="Unaffected", required=False, nullable=True) + + +class TP53SomaticDetails(models.Base): + age = fields.IntField(help_text="Age", required=False, nullable=True) + country = fields.StringField(help_text="Country", required=False, nullable=True) + effect = fields.StringField(help_text="Effect", required=False, nullable=True) + morphology = fields.StringField(help_text="Morphology", required=False, nullable=True) + mut_rate = fields.IntField(help_text="Mutation rate", required=False, nullable=True) + pub_med_references = fields.ListField(items_types=(int,), help_text="PubMed References", required=False, + nullable=True) + sample_source = fields.StringField(help_text="Sample source", required=False, nullable=True) + stage = fields.StringField(help_text="Stage", required=False, nullable=True) + structural_motif = fields.StringField(help_text="Structural Motif", required=False, nullable=True) + topography = fields.StringField(help_text="Topography", required=False, nullable=True) + + +class TP53Germline(models.Base): + version = fields.StringField(help_text="Version") + items = fields.ListField(help_text='Details', items_types=(TP53GermlineDetails,)) + + +class TP53Somatic(models.Base): + version = fields.StringField(help_text="Version") + items = fields.ListField(help_text='Details', items_types=(TP53SomaticDetails,)) diff --git a/varsome_api/models/elements/icgc.py b/varsome_api/models/elements/icgc.py new file mode 100755 index 0000000..8cfbaa0 --- /dev/null +++ b/varsome_api/models/elements/icgc.py @@ -0,0 +1,32 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from jsonmodels import models, fields + +__author__ = "ckopanos" + + +class Occurrence(models.Base): + affected = fields.IntField(required=False, nullable=True, help_text="Affected number") + donors = fields.IntField(required=False, nullable=True, help_text="Donors number") + project = fields.StringField(required=False, nullable=True, help_text="Project") + + +class Somatic(models.Base): + version = fields.StringField(help_text="Version") + id = fields.StringField(help_text="ID", required=False, nullable=True) + occurrence = fields.ListField(required=False, nullable=True, items_types=(Occurrence, ), help_text="Occurrence") + affected_donors = fields.IntField(help_text="Affected Donors", required=False, nullable=True) + project_count = fields.IntField(help_text="Project Count", required=False, nullable=True) + main_data = fields.StringField(help_text="Main data point", required=False, nullable=True) \ No newline at end of file diff --git a/varsome_api/models/elements/isb.py b/varsome_api/models/elements/isb.py new file mode 100755 index 0000000..33897c8 --- /dev/null +++ b/varsome_api/models/elements/isb.py @@ -0,0 +1,24 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from jsonmodels import models, fields + +__author__ = "ckopanos" + + +class Kaviar3(models.Base): + version = fields.StringField(help_text="Version") + ac = fields.ListField(items_types=(int, ), help_text="ac", required=False, nullable=True) + an = fields.ListField(items_types=(int,), help_text="an", required=False, nullable=True) + main_data = fields.StringField(help_text="Main data point", required=False) \ No newline at end of file diff --git a/varsome_api/models/elements/ncbi.py b/varsome_api/models/elements/ncbi.py new file mode 100755 index 0000000..7b758f8 --- /dev/null +++ b/varsome_api/models/elements/ncbi.py @@ -0,0 +1,40 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from jsonmodels import models, fields + +from varsome_api.models.fields import DictField + +__author__ = "ckopanos" + + +class DbSNP(models.Base): + version = fields.StringField(help_text="Version") + rsid = fields.ListField(items_types=(int,), help_text="RS ID") + + +class ClinVar2(models.Base): + version = fields.StringField(help_text="Version") + review_status = fields.StringField(help_text="Review status", required=False, nullable=True) + review_stars = fields.IntField(help_text="Review stars", required=False, nullable=True) + variation_id = fields.IntField(help_text="Variation ID", required=False, nullable=True) + num_submitters = fields.IntField(help_text="Number of submitters", required=False, nullable=True) + pub_med_references = fields.ListField(items_types=(int,), help_text="PubMed references", required=False, + nullable=True) + clinical_significance = fields.ListField(items_types=(str,), help_text="Clinical significance", required=False, + nullable=True) + last_evaluation = fields.StringField(help_text="Last evaluation", required=False, nullable=True) + origin = fields.ListField(items_types=(str,), help_text="Origin", required=False, nullable=True) + accessions = fields.ListField(items_types=(dict,), help_text="Accessions", required=False, nullable=True) + main_data = fields.StringField(help_text="Main data point", required=False, nullable=True) diff --git a/varsome_api/models/elements/sanger.py b/varsome_api/models/elements/sanger.py new file mode 100755 index 0000000..de8a12f --- /dev/null +++ b/varsome_api/models/elements/sanger.py @@ -0,0 +1,96 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from jsonmodels import models, fields + +__author__ = "ckopanos" + + +class Cosmic(models.Base): + version = fields.StringField(help_text="Version") + primary_site = fields.ListField(items_types=(str,), help_text="Primary site", required=False, nullable=True) + pub_med_references = fields.ListField(items_types=(int,), help_text="PUBMED References", required=False, + nullable=True) + + +class CosmicLicensedDrugEntry(models.Base): + drug_name = fields.StringField(help_text="Drug name", required=False, nullable=True) + somatic_status = fields.StringField(help_text="Somatic status", required=False, nullable=True) + zygosity = fields.StringField(help_text="Zygosity", required=False, nullable=True) + gene = fields.StringField(help_text="Gene", required=False, nullable=True) + transcript = fields.StringField(help_text="Transcript", required=False, nullable=True) + census_gene = fields.StringField(help_text="Census gene", required=False, nullable=True) + pub_med_references = fields.ListField(items_types=(int,), help_text="PUBMED References", required=False, + nullable=True) + histology_freq = fields.ListField(items_types=(float,), help_text="Histology frequency", required=False, + nullable=True) + tissue_freq = fields.ListField(items_types=(float,), help_text="Tissue frequency", required=False, nullable=True) + + +class CosmicLicensedDetails(models.Base): + entry_type = fields.StringField(help_text="Entry type", required=False, nullable=True) + cosmic_id = fields.ListField(items_types=(str,), help_text="Cosmic ID", required=False, nullable=True) + pub_med_references = fields.ListField(items_types=(int,), help_text="PUBMED References", required=False, + nullable=True) + histology_freq = fields.ListField(items_types=(int, str, float), help_text="Histology frequency", required=False, + nullable=True) + genome_wide_screen_freq = fields.ListField(items_types=(int, str, float), help_text="Histology frequency", required=False, + nullable=True) + loh_freq = fields.ListField(items_types=(int, str, float), help_text="LOH frequency", required=False, nullable=True) + age_freq = fields.ListField(items_types=(int, str, float), help_text="Age frequency", required=False, nullable=True) + zygosity_freq = fields.ListField(items_types=(int, str, float), help_text="Zygosity frequency", required=False, + nullable=True) + tumour_origin_freq = fields.ListField(items_types=(int, str, float,), help_text="Tumour original frequency", required=False, + nullable=True) + somatic_status_freq = fields.ListField(items_types=(int, str, float), help_text="Somatic status frequency", required=False, + nullable=True) + primary_site_freq = fields.ListField(items_types=(int, str, float), help_text="Primary site frequency", required=False, nullable=True) + description = fields.ListField(items_types=(str,), help_text="Description", required=False, nullable=True) + accession_number = fields.ListField(items_types=(str,), help_text="Accession number", required=False, nullable=True) + fathmm_prediction = fields.StringField(help_text="FATHMM prediction", required=False, nullable=True) + fathmm_score = fields.FloatField(help_text="FATHMM score", required=False, nullable=True) + num_entries = fields.IntField(help_text="Number of entries", required=False, nullable=True) + num_samples = fields.IntField(help_text="Number of samples", required=False, nullable=True) + gene = fields.ListField(items_types=(str,), help_text="Gene", required=False, nullable=True) + + fathmm_mkl_coding_score = fields.FloatField(help_text="FATHMM_MKL coding score", required=False, nullable=True) + fathmm_mkl_coding_groups = fields.StringField(help_text="FATHMM_MKL coding groups", required=False, nullable=True) + fathmm_mkl_non_coding_score = fields.FloatField(help_text="FATHMM_MKL non coding score", required=False, + nullable=True) + fathmm_mkl_non_coding_groups = fields.StringField(help_text="FATHMM_MKL non coding groups", required=False, + nullable=True) + whole_exome_freq = fields.ListField(items_types=(str, int, float,), help_text="Whole exome frequency", required=False, + nullable=True) + whole_genome_reseq_freq = fields.ListField(items_types=(str, int, float,), help_text="Whole genome reseq frequency", + required=False, nullable=True) + + resistance_mutation = fields.ListField(items_types=(str,), help_text="Resistance mutation", required=False, + nullable=True) + drug_entries = fields.ListField(items_types=(CosmicLicensedDrugEntry,), help_text="Drug entries", required=False, + nullable=True) + + +class ComsicPublicDetails(models.Base): + num_samples = fields.IntField(help_text='Number of samples') + id = fields.StringField(help_text='Cosmic ID') + + +class CosmicPublic(models.Base): + version = fields.StringField(help_text="Version") + items = fields.ListField(items_types=(ComsicPublicDetails, ), help_text="Details", required=False, nullable=True) + + +class CosmicLicensed(models.Base): + version = fields.StringField(help_text="Version") + items = fields.ListField(items_types=(CosmicLicensedDetails,), help_text="Details") diff --git a/varsome_api/models/elements/thousand_genomes.py b/varsome_api/models/elements/thousand_genomes.py new file mode 100755 index 0000000..20e79cf --- /dev/null +++ b/varsome_api/models/elements/thousand_genomes.py @@ -0,0 +1,35 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from jsonmodels import models, fields + +__author__ = "ckopanos" + + +class ThousandGenomes(models.Base): + version = fields.StringField(help_text="Version") + ac = fields.ListField(items_types=(int,), help_text="Allele Count", required=False, nullable=True) + af = fields.ListField(items_types=(float,), help_text="Allele Frequency", required=False, nullable=True) + an = fields.ListField(items_types=(int,), help_text="Allele Number", required=False, nullable=True) + ns = fields.ListField(items_types=(int,), help_text="Number of Samples", required=False, nullable=True) + afr_af = fields.ListField(items_types=(float,), help_text="Allele Frequency African", required=False, nullable=True) + amr_af = fields.ListField(items_types=(float,), help_text="Allele Frequency American", required=False, + nullable=True) + eas_af = fields.ListField(items_types=(float,), help_text="Allele Frequency East Asian", required=False, + nullable=True) + eur_af = fields.ListField(items_types=(float,), help_text="Allele Frequency European", required=False, + nullable=True) + sas_af = fields.ListField(items_types=(float,), help_text="Allele Frequency South Asian", required=False, + nullable=True) + main_data = fields.StringField(help_text="Main data point", required=False, nullable=True) diff --git a/varsome_api/models/elements/transcript.py b/varsome_api/models/elements/transcript.py new file mode 100755 index 0000000..0b9b2af --- /dev/null +++ b/varsome_api/models/elements/transcript.py @@ -0,0 +1,37 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + + +from jsonmodels import models, fields + +__author__ = "ckopanos" + + +class TranscriptItem(models.Base): + name = fields.StringField(help_text="Transcript") + coding_impact = fields.StringField(help_text="Coding impact", required=False, nullable=True) + function = fields.ListField(help_text="Function", items_types=(str,), required=False, nullable=True) + hgvs = fields.StringField(required=False, help_text="HGVS cDNA level", nullable=True) + hgvs_p1 = fields.StringField(required=False, nullable=True) + hgvs_p3 = fields.StringField(required=False, nullable=True) + hgvs_notation = fields.StringField(help_text="HGVS notation", required=False, nullable=True) + location = fields.StringField(help_text="Location", required=False, nullable=True) + coding_location = fields.StringField(help_text="Coding location", required=False, nullable=True) + canonical = fields.BoolField(help_text="Canonical", required=False, nullable=True) + gene_symbol = fields.StringField(help_text="Gene symbol", required=False, nullable=True) + + +class Transcript(models.Base): + items = fields.ListField(help_text='Transcripts', items_types=(TranscriptItem,), required=False) + version = fields.StringField(help_text="Version") diff --git a/varsome_api/models/elements/uniprot.py b/varsome_api/models/elements/uniprot.py new file mode 100755 index 0000000..30855da --- /dev/null +++ b/varsome_api/models/elements/uniprot.py @@ -0,0 +1,36 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + + +from jsonmodels import models, fields + +__author__ = "ckopanos" + + +class UniprotVariantsDetails(models.Base): + annotation_id = fields.StringField(help_text="Annotation ID", required=False, nullable=True) + protein_id = fields.StringField(help_text="Protein ID", required=False, nullable=True) + bed_comments = fields.ListField(help_text="Comments", items_types=(str, ), required=False, nullable=True) + gene = fields.StringField(help_text="Gene", required=False, nullable=True) + variant_type = fields.StringField(help_text="Variant type", required=False, nullable=True) + transcripts = fields.ListField(help_text="Transcripts", items_types=(str,), required=False, nullable=True) + pub_med_references = fields.ListField(help_text="PubMed References", items_types=(int,), required=False, nullable=True) + disease = fields.StringField(help_text="Disease", required=False, nullable=True) + disease_symbol = fields.StringField(help_text="Disease symbol", required=False, nullable=True) + disease_alt_symbol = fields.StringField(help_text="Disease alt symbol", required=False, nullable=True) + + +class UniprotVariants(models.Base): + version = fields.StringField(help_text="Version") + items = fields.ListField(help_text='Details', items_types=(UniprotVariantsDetails,)) diff --git a/varsome_api/models/elements/wustl.py b/varsome_api/models/elements/wustl.py new file mode 100755 index 0000000..e2633d7 --- /dev/null +++ b/varsome_api/models/elements/wustl.py @@ -0,0 +1,46 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from jsonmodels import models, fields + +__author__ = "ckopanos" + + +class CivicDetails(models.Base): + variant = fields.StringField(help_text="Variant", required=False, nullable=True) + variant_summary = fields.StringField(help_text="Variant summary", required=False, nullable=True) + variant_civic_url = fields.StringField(help_text="Variant CIViC URL", required=False, nullable=True) + variant_origin = fields.StringField(help_text="Variant origin", required=False, nullable=True) + pub_med_references = fields.ListField(items_types=(int, ), help_text="PubMed References", required=False, nullable=True) + clinical_significance = fields.StringField(help_text="Clinical significance", required=False, nullable=True) + evidence_level = fields.StringField(help_text="Evidence level", required=False, nullable=True) + evidence_statement = fields.StringField(help_text="Evidence statement", required=False, nullable=True) + evidence_type = fields.StringField(help_text="Evidence type", required=False, nullable=True) + evidence_status = fields.StringField(help_text="Evidence status", required=False, nullable=True) + evidence_direction = fields.StringField(help_text="Evidence direction", required=False, nullable=True) + evidence_civic_url = fields.StringField(help_text="Evidence CIViC URL", required=False, nullable=True) + drugs = fields.ListField(items_types=(str, ), help_text="Drugs", required=False, nullable=True) + transcripts = fields.ListField(items_types=(str, ), help_text="Transcripts", required=False, nullable=True) + representative_transcript = fields.StringField(help_text="Representative transcript", required=False, nullable=True) + disease = fields.StringField(help_text="Disease", required=False, nullable=True) + rating = fields.StringField(help_text="Rating", required=False, nullable=True) + gene = fields.StringField(help_text="Gene", required=False, nullable=True) + gene_civic_url = fields.StringField(help_text="Gene CIViC URL", required=False, nullable=True) + entrez_id = fields.StringField(help_text="Entrez ID", required=False, nullable=True) + doid = fields.StringField(help_text="DOID", required=False, nullable=True) + + +class Civic(models.Base): + version = fields.StringField(help_text="Version") + items = fields.ListField(help_text='Details', items_types=(CivicDetails, )) \ No newline at end of file diff --git a/varsome_api/models/fields.py b/varsome_api/models/fields.py new file mode 100755 index 0000000..a3e8f23 --- /dev/null +++ b/varsome_api/models/fields.py @@ -0,0 +1,23 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +from jsonmodels import fields + +__author__ = "ckopanos" + + +class DictField(fields.BaseField): + + types = (dict,) + diff --git a/varsome_api/models/variant.py b/varsome_api/models/variant.py new file mode 100755 index 0000000..bdc19a2 --- /dev/null +++ b/varsome_api/models/variant.py @@ -0,0 +1,139 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + + +from .fields import DictField +from .elements import * + +__author__ = "ckopanos" + + +class AnnotatedVariant(models.Base): + """ + Base variant result definition model + Most fields are defined as list fields, even though they contain a single list item + This is due to the fact that VarSome API can return both current and old versions of databases + """ + + chromosome = fields.StringField(help_text="Chromosome") + alt = fields.StringField(help_text="ALT Sequence", required=False, nullable=True) + ref = fields.StringField(help_text="REF Sequence", required=False, nullable=True) + pos = fields.IntField(help_text="Position") + variant_id = fields.StringField(help_text='Variant Id') + refseq_transcripts = fields.ListField(required=False, items_types=(Transcript,), help_text="RefSeq Transcripts") + ensembl_transcripts = fields.ListField(required=False, items_types=(Transcript,), help_text="Ensembl Transcripts") + broad_exac = fields.ListField(required=False, items_types=(ExAC,), help_text="ExAC") + gnomad_exomes = fields.ListField(required=False, items_types=(GnomAD,), help_text="gnomAD Exomes (ExAC)") + gnomad_exomes_coverage = fields.ListField(required=False, items_types=(GnomADCoverage,), + help_text="gnomAD exomes coverage") + gnomad_genomes = fields.ListField(required=False, items_types=(GnomAD,), help_text="gnomAD Genomes") + gnomad_genomes_coverage = fields.ListField(required=False, items_types=(GnomADCoverage,), + help_text="gnomAD genomes coverage") + thousand_genomes = fields.ListField(required=False, items_types=(ThousandGenomes,), help_text="1000 Genomes") + gerp = fields.ListField(required=False, items_types=(Gerp,), help_text="GERP") + isb_kaviar3 = fields.ListField(required=False, items_types=(Kaviar3,), help_text='ISB Kaviar3') + dbnsfp = fields.ListField(required=False, items_types=(DbNSFP,), help_text="dbNSFP") + dann_snvs = fields.ListField(required=False, items_types=(DannSNVs,), help_text="DANN score") + dbnsfp_dbscsnv = fields.ListField(required=False, items_types=(DBscSNV,), help_text='dbNSFP dbscSNV') + ncbi_dbsnp = fields.ListField(required=False, items_types=(DbSNP,), help_text="dbSNP") + sanger_cosmic = fields.ListField(required=False, items_types=(Cosmic,), help_text="Sanger Cosmic") + sanger_cosmic_public = fields.ListField(required=False, items_types=(CosmicPublic,), help_text="Cosmic") + sanger_cosmic_licensed = fields.ListField(required=False, items_types=(CosmicLicensed,), help_text="Cosmic") + ncbi_clinvar2 = fields.ListField(required=False, items_types=(ClinVar2,), help_text="ClinVar2") + icgc_somatic = fields.ListField(required=False, items_types=(Somatic,), help_text="ICGC Somatic") + iarc_tp53_germline = fields.ListField(required=False, items_types=(TP53Germline,), help_text="IARC TP53 Germline") + iarc_tp53_somatic = fields.ListField(required=False, items_types=(TP53Somatic,), help_text="IARC TP53 Somatic") + pub_med_articles = DictField(required=False, help_text="PUBMED Articles") + uniprot_variants = fields.ListField(required=False, items_types=(UniprotVariants,), help_text="UniProt variants") + wustl_civic = fields.ListField(required=False, items_types=(Civic,), help_text="CIViC") + gwas = fields.ListField(required=False, items_types=(GWAS,), help_text="GWAS") + + @property + def genes(self): + """ + + :return: list of genes + """ + genes = [] + genes.extend(self.refseq_genes) + genes.extend(self.ensembl_genes) + return list(set(genes)) + + @property + def refseq_genes(self): + """ + + :return: list of genes found in RefSeq transcripts + """ + genes = [] + for transcript in self.refseq_transcripts: + genes.extend([item.gene_symbol for item in transcript.items if item.gene_symbol]) + return genes + + @property + def ensembl_genes(self): + """ + + :return: list of genes found in Ensembl transcripts + """ + genes = [] + for transcript in self.ensembl_transcripts: + genes.extend([item.gene_symbol for item in transcript.items if item.gene_symbol]) + return genes + + @property + def rs_ids(self): + """ + + :return: list of rsids (str) + """ + rs_ids = [] + for dbnsp_entry in self.ncbi_dbsnp: + rs_ids.extend(dbnsp_entry.rsid) + return ["rs%s" % rs_id for rs_id in rs_ids] + + @property + def gnomad_exomes_af(self): + """ + Returns the gnomad exomes af value. + :return: float gnomad exomes af + """ + af = [gnomad_exomes.af for gnomad_exomes in self.gnomad_exomes] + return af[0] if af else None + + @property + def gnomad_genomes_af(self): + """ + Returns the gnomad genomes af value. + :return: float gnomad genomes af + """ + af = [gnomad_genomes.af for gnomad_genomes in self.gnomad_genomes] + return af[0] if af else None + + @property + def gnomad_exomes_an(self): + """ + + :return: int gnomad exomes an + """ + an = [gnomad_exomes.an for gnomad_exomes in self.gnomad_exomes] + return an[0] if an else None + + @property + def gnomad_genomes_an(self): + """ + :return: int gnomad genomes an + """ + an = [gnomad_genomes.an for gnomad_genomes in self.gnomad_genomes] + return an[0] if an else None diff --git a/varsome_api/tests/__init__.py b/varsome_api/tests/__init__.py new file mode 100644 index 0000000..da44d8e --- /dev/null +++ b/varsome_api/tests/__init__.py @@ -0,0 +1 @@ +__author__ = "ckopanos" \ No newline at end of file diff --git a/varsome_api/tests/test_client.py b/varsome_api/tests/test_client.py new file mode 100644 index 0000000..8f736f4 --- /dev/null +++ b/varsome_api/tests/test_client.py @@ -0,0 +1,155 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + + +import os + +import unittest +from tempfile import NamedTemporaryFile +try: + unittest.TestCase.subTest +except AttributeError: + import unittest2 as unittest + +import vcf +from vcf.parser import _Info +from varsome_api.client import VarSomeAPIClient, VarSomeAPIException +from varsome_api.models.variant import AnnotatedVariant +from varsome_api.vcf import VCFAnnotator + +__author__ = "ckopanos" + + +API_KEY = os.getenv('VARSOME_API_KEY', None) +BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) +VARIANTS_CSV_FILE = os.path.join(BASE_DIR, 'tests', 'variants.csv') +VARIANTS_VCF_FILE = os.path.join(BASE_DIR, 'tests', 'variants.vcf') + + + +class TestApiClient(unittest.TestCase): + + def __init__(self, methodName='runTest'): + super().__init__(methodName) + self.client = VarSomeAPIClient(API_KEY) + with open(VARIANTS_CSV_FILE) as f: + self.variants_to_lookup = f.read().splitlines() + if API_KEY is None: + # just get 5 variants without an API key tests might fail with 429 + self.variants_to_lookup = self.variants_to_lookup[:5] + else: + self.variants_to_lookup = self.variants_to_lookup[:50] + + def test_schema(self): + """Check we receive the response schema back""" + self.assertIsNotNone(self.client.schema()) + self.client.session.close() + + def test_404(self): + """Check we can raise VarSomeAPIException""" + with self.assertRaises(VarSomeAPIException) as ve: + self.client.lookup('chrM:410:A:T', ref_genome='hg64') + test_exception = ve.exception + self.assertEqual(test_exception.status, 404) + self.client.session.close() + + def test_get_lookup_hg19(self): + """Check we can do plain get requests""" + for i, variant in enumerate(self.variants_to_lookup): + with self.subTest(i=i): + result = self.client.lookup(variant, ref_genome='hg19', params={'add-all-data': 1, + 'expand-pubmed-articles': 0}) + self.assertIsNotNone(result) + self.assertTrue('variant_id' in result) + self.client.session.close() + + def test_batch_lookup_hg19(self): + """Check we can do batch requests""" + results = self.client.batch_lookup(self.variants_to_lookup, ref_genome='hg19', + params={'add-all-data': 1, 'expand-pubmed-articles': 0}, + raise_exceptions=True) + self.assertEqual(len(results), len(self.variants_to_lookup)) + self.client.session.close() + + +class TestApiResponse(unittest.TestCase): + + def __init__(self, methodName='runTest'): + super().__init__(methodName) + client = VarSomeAPIClient(API_KEY, max_variants_per_batch=1000) + with open(VARIANTS_CSV_FILE) as f: + self.variants_to_lookup = f.read().splitlines() + self.results = client.batch_lookup(self.variants_to_lookup, ref_genome='hg19', + params={'add-all-data': 1, 'expand-pubmed-articles': 0}, + raise_exceptions=True) + client.session.close() + + def test_result_is_not_none(self): + """Check result is not None""" + for i, result in enumerate(self.results): + with self.subTest(i=i): + self.assertIsNotNone(result) + + def test_result_has_variant_id(self): + """Check result includes variant_id""" + for i, result in enumerate(self.results): + with self.subTest(i=i): + self.assertTrue('variant_id' in result) + + def test_variant_chromosome_result_chromosome(self): + """Check that the requested chromosome is the same as the one returned""" + for i, result in enumerate(self.results): + with self.subTest(i=i): + chromosome = self.variants_to_lookup[i].split(":")[0] + self.assertEqual(result['chromosome'], chromosome) + + def test_result_wrapper(self): + """Check that we can wrap the result in a json model""" + for i, result in enumerate(self.results): + with self.subTest(i=i): + annotated_variant = AnnotatedVariant(**result) + self.assertEqual(annotated_variant.chromosome, result['chromosome']) + self.assertIsNotNone(annotated_variant.pos) + self.assertEqual(result['pos'], annotated_variant.pos) + + +class TestVCFAnnotator(VCFAnnotator): + + def annotate_record(self, record, variant_result): + record.INFO['gnomad_genomes_AN'] = variant_result.gnomad_genomes_an + return record + + def add_vcf_header_info(self, vcf_template): + vcf_template.infos['gnomad_genomes_AN'] = _Info('gnomad_genomes_AN', '.', 'Integer', + 'GnomAD genomes allele number value', None, None) + +class TestVcfAnnotator(unittest.TestCase): + + def __init__(self, methodName='runTest'): + super().__init__(methodName) + self.annotator = TestVCFAnnotator(API_KEY) + + def test_annotate_vcf(self): + """Check that we can annotate a vcf file""" + output_vcf_file = NamedTemporaryFile(delete=False) + output_vcf_file.close() + self.annotator.annotate(VARIANTS_VCF_FILE, output_vcf_file.name) + vcf_reader = vcf.Reader(filename=output_vcf_file.name, strict_whitespace=True) + self.assertTrue('gnomad_genomes_AN' in vcf_reader.infos) + for i, record in enumerate(vcf_reader): + with self.subTest(i=i): + self.assertTrue('gnomad_genomes_AN' in record.INFO) + vcf_reader._reader.close() + self.annotator.session.close() + diff --git a/varsome_api/tests/variants.csv b/varsome_api/tests/variants.csv new file mode 100644 index 0000000..22266e1 --- /dev/null +++ b/varsome_api/tests/variants.csv @@ -0,0 +1,3000 @@ +chr18:31400047:A:G +chr9:33797928:G:GCC +chr9:108419525:T:A +chr8:42798225:T:G +chr5:158703735:T:C +chr12:125451487:C:T +chrX:53055916:A:G +chr10:15505648:C:A +chr1:81398346:A:C +chr11:34134595:A:T +chr1:202573181:C:A +chr14:36622555:G:A +chr2:115578379:C:T +chr17:44317259:C:A +chr1:179630010:G:A +chrX:19380975:TA:T +chr2:59847178:C:T +chr1:200182664:C:T +chr4:37823502:TAAAAAAAAAA:T +chr14:41832822:C:A +chr20:2198507:G:T +chr3:41599916:C:A 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+chr12:88787112:C:T \ No newline at end of file diff --git a/varsome_api/tests/variants.vcf b/varsome_api/tests/variants.vcf new file mode 100644 index 0000000..906a5b4 --- /dev/null +++ b/varsome_api/tests/variants.vcf @@ -0,0 +1,156 @@ +##fileformat=VCFv4.1 +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[reads.bam] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=[chr22:42020321-42527953] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/data/reference/ucsc/hg19/ucsc.hg19.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=CALCULATE_AS_NECESSARY baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=2 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=gatk.log help=false genotype_likelihoods_model=SNP p_nonref_model=EXACT heterozygosity=0.001 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.15 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name=dbsnp source=/data/reference/dbSNP_132/dbsnp_132.hg19.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false" +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##reference=file:///data/reference/ucsc/hg19/ucsc.hg19.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BLANK NA12878 NA12891 NA12892 NA19238 NA19239 NA19240 +chr22 42522392 rs28371738 G A 2951.95 . AC=2;AF=0.143;AN=14;BaseQRankSum=0.375;DB;DP=1506;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=123.5516;MQ=253.92;MQ0=0;MQRankSum=0.685;QD=5.90;ReadPosRankSum=0.590 GT:AD:DP:GQ:PL 0/0:6,0:6:18.04:0,18,211 0/1:138,107:250:99:1961,0,3049 0/1:169,77:250:99:1038,0,3533 0/0:249,0:250:99:0,600,5732 0/0:248,1:250:99:0,627,6191 0/0:250,0:250:99:0,615,5899 0/0:250,0:250:99:0,579,5674 +chr22 42522613 rs1135840 G C 11611.03 . AC=6;AF=0.429;AN=14;BaseQRankSum=16.289;DB;DP=1518;DS;Dels=0.03;FS=0.000;HRun=0;HaplotypeScore=142.5716;MQ=242.46;MQ0=0;MQRankSum=2.010;QD=9.16;ReadPosRankSum=-1.731 GT:AD:DP:GQ:PL 0/1:13,4:17:62.64:63,0,296 0/1:118,127:246:99:2396,0,1719 0/0:241,0:244:99:0,459,4476 0/1:161,85:246:99:1489,0,2353 0/1:110,132:242:99:2561,0,1488 0/1:106,135:242:99:2613,0,1389 0/1:116,126:243:99:2489,0,1537 +chr22 42522755 . C G 36.98 . AC=1;AF=0.071;AN=14;BaseQRankSum=-14.866;DP=1527;DS;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=253.4254;MQ=197.36;MQ0=2;MQRankSum=-10.810;QD=0.15;ReadPosRankSum=-17.244 GT:AD:DP:GQ:PL 0/0:26,1:27:51.08:0,51,570 0/0:208,40:248:99:0,236,4169 0/0:192,56:249:99:0,114,4292 0/1:179,66:245:75.42:75,0,3683 0/0:214,32:246:99:0,172,4235 0/0:200,49:249:61.05:0,61,4049 0/0:195,50:246:32.07:0,32,3757 +chr22 42523003 rs116917064 A G 7113.55 . AC=8;AF=0.571;AN=14;BaseQRankSum=6.026;DB;DP=1433;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=101.7894;MQ=182.04;MQ0=0;MQRankSum=-2.501;QD=4.96;ReadPosRankSum=8.294 GT:AD:DP:GQ:PL 0/1:10,2:12:0.62:1,0,257 1/1:9,173:183:99:2385,273,0 0/1:153,95:249:99:355,0,2355 0/1:140,110:250:99:1334,0,2242 0/1:164,85:249:99:1070,0,2279 0/1:160,90:250:99:1245,0,2300 0/1:156,81:238:99:724,0,2764 +chr22 42523077 . A G 54.31 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.563;DP=1521;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=54.8434;MQ=164.04;MQ0=1;MQRankSum=-2.419;QD=2.59;ReadPosRankSum=-1.229 GT:AD:DP:GQ:PL 0/1:17,4:21:92.74:93,0,533 0/0:249,1:250:99:0,544,6985 0/0:250,0:250:99:0,577,6968 0/0:248,2:250:99:0,605,7687 0/0:248,1:249:99:0,583,7300 0/0:246,2:249:99:0,626,7473 0/0:248,1:249:99:0,594,7553 +chr22 42523209 rs28371730 T C 15556.89 . AC=8;AF=0.571;AN=14;BaseQRankSum=3.458;DB;DP=1509;DS;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=120.8206;MQ=221.07;MQ0=0;MQRankSum=-4.945;QD=10.31;ReadPosRankSum=0.639 GT:AD:DP:GQ:PL 0/1:3,6:9:99:154,0,101 1/1:6,237:247:99:4532,308,0 0/1:130,117:248:99:1399,0,3147 0/1:112,129:244:99:2641,0,2556 0/1:115,127:247:99:2320,0,2526 0/1:115,128:248:99:2546,0,2520 0/1:143,104:249:99:1965,0,3288 +chr22 42523211 rs2004511 T C 2445.52 . AC=2;AF=0.143;AN=14;BaseQRankSum=10.587;DB;DP=1509;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=102.7564;MQ=221.50;MQ0=0;MQRankSum=-6.926;QD=4.89;ReadPosRankSum=2.057 GT:AD:DP:GQ:PL 0/0:9,0:9:24.06:0,24,289 0/1:136,113:250:99:1384,0,2176 0/1:146,104:250:99:1108,0,2809 0/0:247,3:250:99:0,439,5546 0/0:245,2:249:99:0,459,5316 0/0:248,2:250:99:0,459,5404 0/0:248,1:250:99:0,533,6069 +chr22 42523409 rs1985842 G T 6801.90 . AC=6;AF=0.429;AN=14;BaseQRankSum=20.509;DB;DP=1454;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=150.8967;MQ=200.12;MQ0=0;MQRankSum=4.472;QD=5.65;ReadPosRankSum=9.396 GT:AD:DP:GQ:PL 0/1:1,3:4:25.84:53,0,26 0/1:153,95:249:99:1597,0,1798 0/0:245,4:250:99:0,336,4079 0/1:168,82:250:99:1339,0,1880 0/1:147,103:250:99:1522,0,1805 0/1:156,94:250:99:1341,0,2322 0/1:129,71:201:99:949,0,2082 +chr22 42523805 rs28371725 C T 1637.33 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.379;DB;DP=1516;DS;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=77.2321;MQ=226.05;MQ0=0;MQRankSum=2.862;QD=6.55;ReadPosRankSum=0.064 GT:AD:DP:GQ:PL 0/0:16,0:16:39.09:0,39,475 0/0:248,1:249:99:0,613,7187 0/1:132,116:248:99:1676,0,2916 0/0:248,0:248:99:0,625,7171 0/0:248,2:250:99:0,604,7252 0/0:250,0:250:99:0,631,7426 0/0:248,1:249:99:0,584,6964 +chr22 42523943 rs16947 A G 23661.10 . AC=8;AF=0.571;AN=14;BaseQRankSum=4.602;DB;DP=1514;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=38.3217;MQ=238.64;MQ0=0;MQRankSum=2.485;QD=15.63;ReadPosRankSum=3.749 GT:AD:DP:GQ:PL 0/1:9,5:14:99:163,0,303 1/1:3,246:250:99:8092,667,0 0/1:129,116:246:99:3190,0,2852 0/1:149,98:247:99:2429,0,3588 0/1:129,118:247:99:3267,0,3052 0/1:122,123:245:99:3428,0,3052 0/1:124,119:244:99:3092,0,2845 +chr22 42524150 . C G 3758.65 . AC=8;AF=0.571;AN=14;BaseQRankSum=24.314;DP=1506;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=172.5901;MQ=242.92;MQ0=0;MQRankSum=11.537;QD=2.50;ReadPosRankSum=-9.185 GT:AD:DP:GQ:PL 1/1:3,3:6:5.98:46,6,0 0/1:161,88:250:99:708,0,300 0/1:161,88:250:99:635,0,308 0/1:160,90:250:99:658,0,229 0/1:180,69:250:99:478,0,113 0/1:176,73:250:99:530,0,271 0/1:170,79:249:99:704,0,133 +chr22 42524435 rs1807313 T A 5252.25 . AC=3;AF=0.214;AN=14;BaseQRankSum=-0.192;DB;DP=1526;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=152.3866;MQ=242.06;MQ0=0;MQRankSum=1.923;QD=9.99;ReadPosRankSum=3.008 GT:AD:DP:GQ:PL 0/1:7,19:26:99:456,0,195 0/0:250,0:250:99:0,698,8167 0/0:246,2:249:99:0,673,7735 0/0:248,2:250:99:0,685,7919 0/0:250,0:250:99:0,688,7814 0/1:120,126:247:99:2539,0,3250 0/1:131,110:246:99:2257,0,3278 +chr22 42524696 rs58440431 T C 6423.61 . AC=2;AF=0.143;AN=14;BaseQRankSum=3.119;DB;DP=1509;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=53.0005;MQ=230.78;MQ0=0;MQRankSum=2.825;QD=12.85;ReadPosRankSum=2.051 GT:AD:DP:GQ:PL 0/0:9,0:9:27.08:0,27,351 0/1:132,116:250:99:3341,0,3914 0/1:141,108:250:99:3082,0,3917 0/0:248,1:250:99:0,692,8578 0/0:250,0:250:99:0,743,8836 0/0:247,2:250:99:0,695,8726 0/0:249,1:250:99:0,699,8650 +chr22 42524947 rs3892097 C T 731.18 . AC=2;AF=0.143;AN=14;BaseQRankSum=0.602;DB;DP=1495;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=154.5421;MQ=217.65;MQ0=0;MQRankSum=4.304;QD=1.47;ReadPosRankSum=1.019 GT:AD:DP:GQ:PL 0/0:3,0:3:8.99:0,9,89 0/1:108,75:244:99:403,0,1684 0/1:125,74:242:99:375,0,2335 0/0:227,1:249:99:0,460,5036 0/0:226,1:247:99:0,448,4884 0/0:192,1:247:99:0,400,4405 0/0:194,1:247:99:0,405,4694 +chr22 42525132 rs1058164 G C 14639.91 . AC=5;AF=0.357;AN=14;BaseQRankSum=4.944;DB;DP=1508;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=38.1229;MQ=207.02;MQ0=6;MQRankSum=2.510;QD=11.71;ReadPosRankSum=0.306 GT:AD:DP:GQ:PL 0/0:8,0:8:24.05:0,24,309 0/1:125,125:250:99:3147,0,3294 0/0:245,1:248:99:0,549,7172 0/1:139,109:248:99:2470,0,3232 0/1:136,107:243:99:2545,0,3408 0/1:116,130:247:99:3206,0,2926 0/1:122,124:247:99:3271,0,3300 +chr22 42525772 rs28371706 G A 7552.52 . AC=4;AF=0.286;AN=14;BaseQRankSum=12.028;DB;DP=1506;DS;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=89.8512;MQ=222.09;MQ0=0;MQRankSum=5.200;QD=9.99;ReadPosRankSum=2.275 GT:AD:DP:GQ:PL 0/1:4,2:6:29.34:29,0,147 0/0:249,0:249:99:0,592,6835 0/0:249,1:250:99:0,590,7041 0/0:248,0:248:99:0,652,7316 0/1:126,120:248:99:2668,0,2833 0/1:134,113:247:99:2453,0,2485 0/1:137,113:250:99:2403,0,2988 +chr22 42525798 rs28371705 G C 1954.58 . AC=2;AF=0.143;AN=14;BaseQRankSum=6.229;DB;DP=1509;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=36.0442;MQ=228.55;MQ0=0;MQRankSum=0.852;QD=3.91;ReadPosRankSum=6.520 GT:AD:DP:GQ:PL 0/0:9,0:9:27.08:0,27,342 0/1:164,85:250:99:981,0,3519 0/1:171,79:250:99:1020,0,3665 0/0:249,1:250:99:0,526,6474 0/0:249,1:250:99:0,550,6481 0/0:248,2:250:99:0,542,6933 0/0:250,0:250:99:0,604,7282 +chr22 42525811 rs28371704 T C 3688.26 . AC=2;AF=0.143;AN=14;BaseQRankSum=4.752;DB;DP=1510;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=36.9902;MQ=210.28;MQ0=0;MQRankSum=2.309;QD=7.38;ReadPosRankSum=6.262 GT:AD:DP:GQ:PL 0/0:10,0:10:27.06:0,27,333 0/1:163,86:249:99:1958,0,3391 0/1:167,78:245:99:1730,0,3945 0/0:248,1:249:99:0,542,6887 0/0:246,1:247:99:0,550,6569 0/0:247,1:250:99:0,548,6954 0/0:249,1:250:99:0,557,7079 +chr22 42525821 rs28371703 G T 3940.90 . AC=2;AF=0.143;AN=14;BaseQRankSum=4.652;DB;DP=1510;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=34.0483;MQ=210.28;MQ0=0;MQRankSum=2.924;QD=7.88;ReadPosRankSum=5.487 GT:AD:DP:GQ:PL 0/0:10,0:10:24.08:0,24,317 0/1:164,85:250:99:2033,0,3659 0/1:167,79:249:99:1907,0,4271 0/0:249,1:250:99:0,565,7321 0/0:249,1:250:99:0,545,7102 0/0:248,2:250:99:0,536,7254 0/0:249,0:250:99:0,605,7633 +chr22 42525952 rs71328650 C A 5872.92 . AC=7;AF=0.500;AN=14;BaseQRankSum=25.986;DB;DP=1505;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=144.2979;MQ=173.55;MQ0=0;MQRankSum=3.660;QD=4.68;ReadPosRankSum=7.152 GT:AD:DP:GQ:PL 1/1:2,3:5:6:53,6,0 0/1:132,117:250:99:1397,0,702 0/0:248,1:250:99:0,245,2219 0/1:166,83:250:99:1151,0,934 0/1:164,86:250:99:1070,0,1147 0/1:170,80:250:99:1009,0,1141 0/1:162,87:250:99:1194,0,1085 +chr22 42526049 . C G 8544.41 . AC=10;AF=0.714;AN=14;BaseQRankSum=-8.121;DP=1505;DS;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=241.7335;MQ=162.18;MQ0=2;MQRankSum=-1.399;QD=6.81;ReadPosRankSum=2.132 GT:AD:DP:GQ:PL 1/1:0,5:5:3:26,3,0 0/1:86,162:248:99:1053,0,1167 0/0:235,12:248:99:0,378,3886 0/1:108,137:245:99:782,0,1662 1/1:3,242:245:99:2351,264,0 1/1:5,245:250:99:2193,222,0 1/1:4,242:246:99:2140,240,0 +chr22 42526449 . T A 151.47 . AC=1;AF=0.071;AN=14;BaseQRankSum=2.662;DP=1226;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=41.2083;MQ=240.47;MQ0=0;MQRankSum=0.578;QD=4.89;ReadPosRankSum=3.611 GT:AD:DP:GQ:PL 0/1:23,8:31:99:190,0,694 0/0:188,0:190:99:0,478,5376 0/0:187,0:187:99:0,493,5322 0/0:247,0:249:99:0,634,6728 0/0:185,0:185:99:0,487,5515 0/0:202,0:202:99:0,520,5857 0/0:181,1:182:99:0,440,5362 +chr22 42526484 rs28371699 A C 4220.99 . AC=6;AF=0.429;AN=14;BaseQRankSum=-17.855;DB;DP=1532;DS;Dels=0.02;FS=0.000;HRun=0;HaplotypeScore=136.8893;MQ=233.92;MQ0=0;MQRankSum=3.448;QD=3.29;ReadPosRankSum=-2.663 GT:AD:DP:GQ:PL 0/1:16,15:31:99:238,0,428 0/1:112,135:247:99:796,0,1908 0/0:227,13:241:99:0,433,4747 0/1:108,133:242:99:588,0,2014 0/1:90,154:245:99:1055,0,1892 0/1:112,131:246:99:741,0,2222 0/1:108,137:246:99:803,0,2266 +chr22 42526549 rs56011157 C T 14276.31 . AC=8;AF=0.571;AN=14;BaseQRankSum=17.750;DB;DP=1537;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=87.3394;MQ=231.34;MQ0=0;MQRankSum=4.781;QD=9.29;ReadPosRankSum=7.463 GT:AD:DP:GQ:PL 0/1:22,15:37:99:251,0,330 1/1:23,227:250:99:5404,430,0 0/1:151,98:250:99:1878,0,2475 0/1:153,97:250:99:1769,0,2410 0/1:149,100:250:99:1792,0,2569 0/1:164,84:250:99:1440,0,2646 0/1:149,98:248:99:1742,0,2601 +chr22 42526561 rs28695233 G T 4524.61 . AC=7;AF=0.500;AN=14;BaseQRankSum=9.714;DB;DP=1538;DS;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=98.8415;MQ=220.45;MQ0=0;MQRankSum=9.430;QD=3.02;ReadPosRankSum=7.682 GT:AD:DP:GQ:PL 0/0:22,15:38:15.74:0,16,609 1/1:4,240:249:99:2685,237,0 0/1:142,108:250:99:505,0,3133 0/1:138,109:249:99:521,0,3281 0/1:150,99:249:99:336,0,3601 0/1:153,93:250:99:194,0,3695 0/1:148,97:249:99:283,0,3093 +chr22 42526562 rs75276289 G C 3780.51 . AC=6;AF=0.429;AN=14;BaseQRankSum=15.200;DB;DP=1540;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=116.4370;MQ=215.67;MQ0=0;MQRankSum=9.072;QD=2.52;ReadPosRankSum=10.863 GT:AD:DP:GQ:PL 0/0:25,15:40:17.73:0,18,633 0/1:50,199:250:99:1522,0,283 0/1:143,106:250:99:600,0,2844 0/1:143,107:250:99:605,0,3002 0/1:151,99:250:99:432,0,3352 0/1:157,93:250:99:254,0,3483 0/1:149,99:248:99:368,0,2999 +chr22 42526567 rs76312385 G A 434.33 . AC=1;AF=0.071;AN=14;BaseQRankSum=18.089;DB;DP=1540;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=89.3746;MQ=219.80;MQ0=0;MQRankSum=6.196;QD=1.74;ReadPosRankSum=7.564 GT:AD:DP:GQ:PL 0/0:22,18:40:4.68:0,5,427 0/1:34,215:250:56.26:473,0,56 0/0:142,108:250:20.78:0,21,2288 0/0:142,108:250:49.48:0,49,2451 0/0:152,97:250:99:0,210,2801 0/0:150,100:250:34.96:0,35,2515 0/0:148,102:250:77.19:0,77,2590 +chr22 42526571 rs74644586 C G 339.60 . AC=1;AF=0.071;AN=14;BaseQRankSum=-11.480;DB;DP=1540;DS;Dels=0.02;FS=0.000;HRun=4;HaplotypeScore=93.3402;MQ=218.52;MQ0=0;MQRankSum=3.709;QD=1.36;ReadPosRankSum=6.322 GT:AD:DP:GQ:PL 0/0:22,18:40:36.46:0,36,689 0/1:4,232:239:30.49:378,0,30 0/0:138,110:249:99:0,295,4017 0/0:137,111:249:99:0,250,4041 0/0:147,97:245:99:0,321,4348 0/0:150,97:247:99:0,358,4657 0/0:144,101:247:99:0,275,4123 +chr22 42526573 rs1080996 T G 12579.34 . AC=8;AF=0.571;AN=14;BaseQRankSum=6.163;DB;DP=1540;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=76.6550;MQ=224.49;MQ0=0;MQRankSum=1.355;QD=8.17;ReadPosRankSum=5.794 GT:AD:DP:GQ:PL 0/1:22,18:40:99:200,0,668 1/1:4,244:248:99:5175,439,0 0/1:136,110:250:99:1862,0,3521 0/1:136,113:249:99:1734,0,3677 0/1:144,99:250:99:1119,0,3818 0/1:150,99:250:99:1196,0,4178 0/1:145,104:250:99:1293,0,3628 +chr22 42526580 rs1080995 G C 16619.47 . AC=8;AF=0.571;AN=14;BaseQRankSum=7.991;DB;DP=1541;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=56.1489;MQ=221.29;MQ0=0;MQRankSum=2.223;QD=10.78;ReadPosRankSum=4.443 GT:AD:DP:GQ:PL 0/1:22,19:41:99:335,0,664 1/1:15,234:250:99:5895,337,0 0/1:137,113:250:99:2421,0,3301 0/1:134,116:250:99:2262,0,3430 0/1:144,105:250:99:1929,0,3421 0/1:148,101:250:99:1778,0,3867 0/1:142,108:250:99:1999,0,3334 +chr22 42526634 . T C 32.60 . AC=1;AF=0.071;AN=14;BaseQRankSum=1.147;DP=1225;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=50.0151;MQ=240.65;MQ0=0;MQRankSum=1.151;QD=1.30;ReadPosRankSum=1.276 GT:AD:DP:GQ:PL 0/1:21,4:25:71.04:71,0,702 0/0:187,2:189:99:0,481,6080 0/0:233,0:233:99:0,667,7351 0/0:230,0:230:99:0,667,7394 0/0:174,1:175:99:0,446,5469 0/0:194,2:196:99:0,498,6239 0/0:174,0:175:99:0,511,5894 +chr22 42526679 . G C 60.60 . AC=1;AF=0.071;AN=14;BaseQRankSum=-12.425;DP=1525;DS;Dels=0.09;FS=0.000;HRun=1;HaplotypeScore=331.3182;MQ=215.48;MQ0=0;MQRankSum=-14.680;QD=0.24;ReadPosRankSum=-13.323 GT:AD:DP:GQ:PL 0/0:23,0:23:66.17:0,66,829 0/1:175,56:232:99:99,0,4273 0/0:199,26:226:76.45:0,76,5104 0/0:196,37:233:41.98:0,42,5109 0/0:170,47:218:99:0,162,4505 0/0:188,36:224:99:0,230,4974 0/0:177,47:225:99:0,167,4592 +chr22 42526694 rs1065852 G A 4420.63 . AC=2;AF=0.143;AN=14;BaseQRankSum=8.566;DB;DP=1529;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=117.6833;MQ=214.96;MQ0=0;MQRankSum=5.852;QD=8.84;ReadPosRankSum=1.454 GT:AD:DP:GQ:PL 0/0:29,0:29:81.24:0,81,1040 0/1:136,114:250:99:2333,0,3170 0/1:145,104:250:99:2087,0,2794 0/0:250,0:250:99:0,586,6963 0/0:247,2:250:99:0,497,6185 0/0:248,2:250:99:0,544,6640 0/0:250,0:250:99:0,571,6444 +chr22 42527471 rs28633410 T C 26831.16 . AC=10;AF=0.833;AN=12;BaseQRankSum=-1.092;DB;DP=1501;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=79.3853;MQ=176.86;MQ0=0;MQRankSum=-2.644;QD=17.89;ReadPosRankSum=2.185 GT:AD:DP:GQ:PL ./. 1/1:1,249:250:99:5741,478,0 0/1:102,148:250:99:3026,0,1748 0/1:115,132:250:99:2716,0,1896 1/1:1,249:250:99:5040,392,0 1/1:1,248:250:99:5109,427,0 1/1:4,245:249:99:5199,306,0 +chr22 42527533 rs28624811 A G 13619.46 . AC=7;AF=0.583;AN=12;BaseQRankSum=-8.893;DB;DP=1501;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=86.1948;MQ=179.18;MQ0=0;MQRankSum=0.472;QD=9.08;ReadPosRankSum=0.778 GT:AD:DP:GQ:PL ./. 1/1:2,241:243:99:4171,416,0 0/1:113,132:245:99:2000,0,2018 0/1:120,126:246:99:1781,0,1970 0/1:131,118:249:99:1885,0,1784 0/1:122,126:248:99:1893,0,1807 0/1:122,127:249:99:1890,0,2119 +chr22 42527793 rs1080989 C T 3454.66 . AC=2;AF=0.167;AN=12;BaseQRankSum=-3.007;DB;DP=1074;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=75.7865;MQ=209.00;MQ0=0;MQRankSum=3.014;QD=9.36;ReadPosRankSum=0.618 GT:AD:DP:GQ:PL ./. 0/1:72,90:162:99:1699,0,1767 0/1:103,96:202:99:1756,0,2532 0/0:188,0:188:99:0,526,5889 0/0:160,0:160:99:0,457,4983 0/0:197,0:198:99:0,544,6100 0/0:156,0:156:99:0,439,5041 +chr22 42527891 . T A 109.83 . AC=5;AF=0.417;AN=12;BaseQRankSum=11.235;DP=1500;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=638.4601;MQ=166.82;MQ0=0;MQRankSum=1.444;QD=0.09;ReadPosRankSum=0.839 GT:AD:DP:GQ:PL ./. 0/1:238,7:248:13.70:14,0,38 0/0:246,3:250:5.97:0,6,45 0/1:239,11:250:31.42:31,0,54 0/1:232,16:250:49.09:49,0,76 0/1:233,14:249:52.10:52,0,53 0/1:238,11:250:12.71:13,0,36 diff --git a/varsome_api/vcf.py b/varsome_api/vcf.py new file mode 100755 index 0000000..752e726 --- /dev/null +++ b/varsome_api/vcf.py @@ -0,0 +1,147 @@ +# Copyright 2018 Saphetor S.A. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + + +import os +import time +import vcf +from collections import OrderedDict +from vcf.parser import _Info +from varsome_api.client import VarSomeAPIClient +from varsome_api.models.variant import AnnotatedVariant + +__author__ = "ckopanos" + + +class VCFAnnotator(VarSomeAPIClient): + """ + VCFAnnotator will take an input vcf file parse it and produce an annotated vcf file + """ + + def __init__(self, api_key=None, + max_variants_per_batch=1000, ref_genome='hg19', get_parameters=None, max_threads=None): + super().__init__(api_key, max_variants_per_batch) + self.ref_genome = ref_genome + self.get_parameters = get_parameters + self.total_varialts = 0 + self.filtered_out_variants = 0 + self.variants_with_errors = 0 + self.max_threads = max_threads or 1 + if self.max_variants_per_batch > 3000 and self.max_threads > 1: + self.logger.warning("Having more than 1 thread with more than 3000 variants per batch may not be optimal") + + def _process_request(self, input_batch): + start = time.time() + api_results = self.batch_lookup(list(input_batch.keys()), params=self.get_parameters, + ref_genome=self.ref_genome, max_threads=self.max_threads) + duration = time.time() - start + self.logger.info('Annotated %s variants in %s' % (len(input_batch), duration)) + self.logger.info('Writing to output vcf file') + for i, requested_variant in enumerate(input_batch.keys()): + try: + results = api_results[i] + record = input_batch[requested_variant] + if results: + if 'filtered_out' in results: + self.logger.info(results['filtered_out']) + self.filtered_out_variants += 1 + continue + if 'error' in results: + self.logger.error(results['error']) + self.variants_with_errors += 1 + continue + if 'variant_id' in results: + variant_result = AnnotatedVariant(**results) + record = self.annotate_record(record, variant_result) + self.vcf_writer.write_record(record) + else: + self.logger.error(results) + self.variants_with_errors += 1 + except Exception as e: + self.logger.error(e) + self.variants_with_errors += 1 + pass # log an exception.. + + def annotate_record(self, record, variant_result): + """ + Method to annotate a record. You should override this with your own implementation + to include variant result properties you want in your output vcf + :param record: vcf record object + :param variant_result: AnnotatedVariant object + :return: annotated record object + """ + record.INFO['variant_id'] = variant_result.variant_id + record.INFO['gene'] = ",".join(variant_result.genes) + record.INFO['gnomad_exomes_AF'] = variant_result.gnomad_exomes_af + record.INFO['gnomad_genomes_AF'] = variant_result.gnomad_genomes_af + record.ALT = variant_result.alt + record.POS = variant_result.pos + record.ID = ";".join(variant_result.rs_ids) or "." + return record + + def add_vcf_header_info(self, vcf_template): + """ + Adds vcf INFO headers for the annotated values provided + This is just a base method you need to override in your own implementation + depending on the annotations added through the annotate_record method + :param vcf_template: vcf reader object + :return: + """ + vcf_template.infos['variant_id'] = _Info('variant_id', 1, 'Integer', 'Saphetor variant identifier', None, None) + vcf_template.infos['gene'] = _Info('gene', '.', 'String', 'Genes related to this variant', None, None) + vcf_template.infos['gnomad_exomes_AF'] = _Info('gnomad_exomes_AF', '.', 'Float', + 'GnomAD exomes allele frequency value', None, None) + vcf_template.infos['gnomad_genomes_AF'] = _Info('gnomad_genomes_AF', '.', 'Float', + 'GnomAD genomes allele frequency value', None, None) + + def annotate(self, input_vcf_file, output_vcf_file=None, template=None, **kwargs): + """ + :param input_vcf_file: The input vcf file to be annotated + :param output_vcf_file: The file to write annotations back if none input_vcf_file.annotated.vcf will be + generated instead + :param template: An alternate vcf file to use for vcf file headers. If none the input vcf file will + be used + :return: + """ + annotations_start = time.time() + if not os.path.isfile(input_vcf_file): + raise FileNotFoundError('%s does not exist' % input_vcf_file) + if output_vcf_file is None: + output_vcf_file = "%s.annotated.vcf" % input_vcf_file + vcf_reader = vcf.Reader(filename=input_vcf_file, strict_whitespace=kwargs.get('strict_whitespace', True)) + vcf_template = vcf_reader if template is None else vcf.Reader(filename=template, strict_whitespace=kwargs.get( + 'strict_whitespace', True)) + self.add_vcf_header_info(vcf_template) + self.vcf_writer = vcf.Writer(open(output_vcf_file, 'w'), vcf_template) + input_batch = OrderedDict() + # this will keep the request queue large enough so that parallel requests will not stop executing + batch_limit = self.max_variants_per_batch * self.max_threads * 2 + for record in vcf_reader: + for alt_seq in record.ALT: + requested_variant = "%s:%s:%s:%s" % (record.CHROM, record.POS, record.REF or "", alt_seq or "") + input_batch[requested_variant] = record + self.total_varialts += 1 + if len(input_batch) < batch_limit: + continue + self._process_request(input_batch) + # reset input batch + input_batch = OrderedDict() + # we may have some variants remaining if input batch is less than batch size + if len(input_batch) > 0: + self._process_request(input_batch) + self.vcf_writer.close() + self.logger.info("Annotating %s variants in %s. " + "Filtered out %s. " + "Errors %s" % (self.total_varialts, time.time() - annotations_start, + self.filtered_out_variants, self.variants_with_errors))