##fileformat=VCFv4.2
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##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.7-0-gcfedb67,Date="Fri Aug 26 20:52:06 CEST 2022",Epoch=1661539926702,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/fast/work/groups/cubi/projects/2022-07-06_VarFish_Course_Data/snappy-processing/ngs_mapping/work/bwa.Case_1_index-N1-DNA1-WGS1/out/bwa.Case_1_index-N1-DNA1-WGS1.bam, /fast/work/groups/cubi/projects/2022-07-06_VarFish_Course_Data/snappy-processing/ngs_mapping/work/bwa.Case_1_father-N1-DNA1-WGS1/out/bwa.Case_1_father-N1-DNA1-WGS1.bam, /fast/work/groups/cubi/projects/2022-07-06_VarFish_Course_Data/snappy-processing/ngs_mapping/work/bwa.Case_1_mother-N1-DNA1-WGS1/out/bwa.Case_1_mother-N1-DNA1-WGS1.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[1:1-5,010,000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/fast/projects/cubit/current/static_data/reference/GRCh37/hs37d5/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 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bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=3 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=true keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null 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##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
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##bcftools_viewCommand=view --header-only /data/gpfs-1/users/holtgrem_c/scratch/tmp/tmp.uG5Q6d0QYe/tmp.vcf.gz; Date=Fri Aug 26 21:03:40 2022
##SAMPLE=<ID=Case_1_index-N1-DNA1-WGS1,Sex=Male,Disease=Affected>
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job_out.574.d/out/tmp_574.vcf.gz job_out.575.d/out/tmp_575.vcf.gz job_out.576.d/out/tmp_576.vcf.gz job_out.577.d/out/tmp_577.vcf.gz job_out.578.d/out/tmp_578.vcf.gz job_out.579.d/out/tmp_579.vcf.gz job_out.580.d/out/tmp_580.vcf.gz job_out.581.d/out/tmp_581.vcf.gz job_out.582.d/out/tmp_582.vcf.gz job_out.583.d/out/tmp_583.vcf.gz job_out.584.d/out/tmp_584.vcf.gz job_out.585.d/out/tmp_585.vcf.gz job_out.586.d/out/tmp_586.vcf.gz job_out.587.d/out/tmp_587.vcf.gz job_out.588.d/out/tmp_588.vcf.gz job_out.589.d/out/tmp_589.vcf.gz job_out.590.d/out/tmp_590.vcf.gz job_out.591.d/out/tmp_591.vcf.gz job_out.592.d/out/tmp_592.vcf.gz job_out.593.d/out/tmp_593.vcf.gz job_out.594.d/out/tmp_594.vcf.gz job_out.595.d/out/tmp_595.vcf.gz job_out.596.d/out/tmp_596.vcf.gz job_out.597.d/out/tmp_597.vcf.gz job_out.598.d/out/tmp_598.vcf.gz job_out.599.d/out/tmp_599.vcf.gz job_out.600.d/out/tmp_600.vcf.gz job_out.601.d/out/tmp_601.vcf.gz job_out.602.d/out/tmp_602.vcf.gz job_out.603.d/out/tmp_603.vcf.gz job_out.604.d/out/tmp_604.vcf.gz job_out.605.d/out/tmp_605.vcf.gz job_out.606.d/out/tmp_606.vcf.gz job_out.607.d/out/tmp_607.vcf.gz job_out.608.d/out/tmp_608.vcf.gz job_out.609.d/out/tmp_609.vcf.gz job_out.610.d/out/tmp_610.vcf.gz job_out.611.d/out/tmp_611.vcf.gz job_out.612.d/out/tmp_612.vcf.gz job_out.613.d/out/tmp_613.vcf.gz job_out.614.d/out/tmp_614.vcf.gz job_out.615.d/out/tmp_615.vcf.gz job_out.616.d/out/tmp_616.vcf.gz job_out.617.d/out/tmp_617.vcf.gz job_out.618.d/out/tmp_618.vcf.gz job_out.619.d/out/tmp_619.vcf.gz job_out.620.d/out/tmp_620.vcf.gz job_out.621.d/out/tmp_621.vcf.gz job_out.622.d/out/tmp_622.vcf.gz job_out.623.d/out/tmp_623.vcf.gz job_out.624.d/out/tmp_624.vcf.gz job_out.625.d/out/tmp_625.vcf.gz job_out.626.d/out/tmp_626.vcf.gz job_out.627.d/out/tmp_627.vcf.gz job_out.628.d/out/tmp_628.vcf.gz job_out.629.d/out/tmp_629.vcf.gz job_out.630.d/out/tmp_630.vcf.gz job_out.631.d/out/tmp_631.vcf.gz job_out.632.d/out/tmp_632.vcf.gz job_out.633.d/out/tmp_633.vcf.gz job_out.634.d/out/tmp_634.vcf.gz job_out.635.d/out/tmp_635.vcf.gz job_out.636.d/out/tmp_636.vcf.gz job_out.637.d/out/tmp_637.vcf.gz job_out.638.d/out/tmp_638.vcf.gz job_out.639.d/out/tmp_639.vcf.gz job_out.640.d/out/tmp_640.vcf.gz job_out.641.d/out/tmp_641.vcf.gz job_out.642.d/out/tmp_642.vcf.gz job_out.643.d/out/tmp_643.vcf.gz job_out.644.d/out/tmp_644.vcf.gz job_out.645.d/out/tmp_645.vcf.gz job_out.646.d/out/tmp_646.vcf.gz job_out.647.d/out/tmp_647.vcf.gz job_out.648.d/out/tmp_648.vcf.gz job_out.649.d/out/tmp_649.vcf.gz job_out.650.d/out/tmp_650.vcf.gz job_out.651.d/out/tmp_651.vcf.gz job_out.652.d/out/tmp_652.vcf.gz job_out.653.d/out/tmp_653.vcf.gz job_out.654.d/out/tmp_654.vcf.gz job_out.655.d/out/tmp_655.vcf.gz job_out.656.d/out/tmp_656.vcf.gz job_out.657.d/out/tmp_657.vcf.gz job_out.658.d/out/tmp_658.vcf.gz job_out.659.d/out/tmp_659.vcf.gz job_out.660.d/out/tmp_660.vcf.gz job_out.661.d/out/tmp_661.vcf.gz job_out.662.d/out/tmp_662.vcf.gz job_out.663.d/out/tmp_663.vcf.gz job_out.664.d/out/tmp_664.vcf.gz job_out.665.d/out/tmp_665.vcf.gz job_out.666.d/out/tmp_666.vcf.gz job_out.667.d/out/tmp_667.vcf.gz job_out.668.d/out/tmp_668.vcf.gz job_out.669.d/out/tmp_669.vcf.gz job_out.670.d/out/tmp_670.vcf.gz job_out.671.d/out/tmp_671.vcf.gz job_out.672.d/out/tmp_672.vcf.gz job_out.673.d/out/tmp_673.vcf.gz job_out.674.d/out/tmp_674.vcf.gz job_out.675.d/out/tmp_675.vcf.gz job_out.676.d/out/tmp_676.vcf.gz job_out.677.d/out/tmp_677.vcf.gz job_out.678.d/out/tmp_678.vcf.gz job_out.679.d/out/tmp_679.vcf.gz job_out.680.d/out/tmp_680.vcf.gz job_out.681.d/out/tmp_681.vcf.gz job_out.682.d/out/tmp_682.vcf.gz job_out.683.d/out/tmp_683.vcf.gz job_out.684.d/out/tmp_684.vcf.gz job_out.685.d/out/tmp_685.vcf.gz job_out.686.d/out/tmp_686.vcf.gz job_out.687.d/out/tmp_687.vcf.gz job_out.688.d/out/tmp_688.vcf.gz job_out.689.d/out/tmp_689.vcf.gz job_out.690.d/out/tmp_690.vcf.gz job_out.691.d/out/tmp_691.vcf.gz job_out.692.d/out/tmp_692.vcf.gz; Date=Fri Aug 26 22:36:04 2022
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Case_1_father-N1-DNA1-WGS1	Case_1_index-N1-DNA1-WGS1	Case_1_mother-N1-DNA1-WGS1
17	41249263	rs1799965	G	A	573.13	.	AC=1;AF=0.167;AN=6;BaseQRankSum=1.38;ClippingRankSum=0;DB;DP=140;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=13.65;ReadPosRankSum=-0.249;SOR=0.766	GT:AD:DP:GQ:PL	0/0:52,0:52:99:0,156,1718	0/0:46,0:46:99:0,138,1589	0/1:21,21:42:99:604,0,604
17	41252332	rs781576075	T	C	945.16	.	AC=2;AF=0.333;AN=6;BaseQRankSum=-0.53;ClippingRankSum=0;DB;DP=93;ExcessHet=3.9794;FS=0.806;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=13.9;ReadPosRankSum=1.905;SOR=0.557	GT:AD:DP:GQ:PL	0/0:25,0:25:75:0,75,849	0/1:14,14:28:99:392,0,403	0/1:19,21:40:99:585,0,539
17	41252691	.	ATATAAT	A	614.13	.	AC=2;AF=0.333;AN=6;BaseQRankSum=0;ClippingRankSum=0;DP=56;ExcessHet=3.9794;FS=4.119;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=16.6;ReadPosRankSum=-1.059;SOR=1.188	GT:AD:DP:GQ:PL	0/0:9,0:9:27:0,27,405	0/1:4,10:14:99:321,0,138	0/1:12,11:23:99:334,0,360
17	41252693	rs377466939	ATAAT	A	285.1	.	AC=1;AF=0.167;AN=6;BaseQRankSum=0.621;ClippingRankSum=0;DB;DP=56;ExcessHet=3.0103;FS=1.37;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=12.96;ReadPosRankSum=-0.885;SOR=1.115	GT:AD:DP:GQ:PL	0/0:9,0:9:27:0,27,349	0/0:14,0:14:42:0,42,543	0/1:11,11:22:99:325,0,337
17	41252695	rs56679756	AAT	A	144.09	.	AC=1;AF=0.167;AN=6;BaseQRankSum=0.458;ClippingRankSum=0;DB;DP=56;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=16.01;ReadPosRankSum=2.99;SOR=0.478	GT:AD:DP:GQ:PL	0/1:3,6:9:79:184,0,79	0/0:14,0:14:42:0,42,571	0/0:22,0:22:66:0,66,876
17	41252696	rs10445319	A	T	144.16	.	AC=2;AF=0.333;AN=6;BaseQRankSum=0.491;ClippingRankSum=0;DB;DP=56;ExcessHet=3.9794;FS=6.692;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=6.27;ReadPosRankSum=0.439;SOR=1.492	GT:AD:DP:GQ:PL	0/1:6,3:9:78:78,0,185	0/1:10,4:14:98:98,0,381	0/0:22,0:22:67:0,67,964
17	41252697	.	A	AT,ATT	3178.86	.	AC=4,2;AF=0.667,0.333;AN=6;BaseQRankSum=-0.199;ClippingRankSum=0;DB;DP=124;ExcessHet=3.0103;FS=0;MLEAC=4,2;MLEAF=0.667,0.333;MQ=60;MQRankSum=0;QD=28.64;ReadPosRankSum=0.656;SOR=0.707	GT:AD:DP:GQ:PL	1/1:0,45,0:45:99:1263,135,0,1256,135,1251	1/2:0,17,16:33:99:994,425,330,425,0,373	1/2:1,11,21:33:99:957,526,464,246,0,216
17	41254393	.	G	T	37.68	.	AC=1;AF=0.167;AN=6;BaseQRankSum=-3.039;ClippingRankSum=0;DP=89;ExcessHet=3.6798;FS=38.246;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=1.02;ReadPosRankSum=2.515;SOR=5.282	GT:AD:DP:GQ:PL	0/1:29,8:37:66:66,0,688	./.:.:.:.:.	0/0:32,3:35:47:0,47,877
17	41273700	.	C	CA	43.64	.	AC=1;AF=0.167;AN=6;BaseQRankSum=0.99;ClippingRankSum=0;DP=49;ExcessHet=3.0103;FS=2.548;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=4.36;ReadPosRankSum=0.975;SOR=1.371	GT:AD:DP:GQ:PL	0/0:14,0:14:42:0,42,274	0/0:6,1:7:10:0,10,104	0/1:5,5:10:65:81,0,65
MT	73	rs869183622	A	G	214037	.	AC=4;AF=0.667;AN=6;BaseQRankSum=6.388;ClippingRankSum=0.003;DB;DP=10415;ExcessHet=0.4576;FS=235.002;MLEAC=4;MLEAF=0.667;MQ=59;MQRankSum=-7.384;QD=34.57;ReadPosRankSum=-7.688;SOR=7.701	GT:AD:DP:GQ:PL	0/0:3975,0:3975:99:0,11927,135527	1/1:0,2871:2871:99:99277,8639,0	1/1:0,3320:3320:99:114798,9985,0
MT	119	.	T	C	281558	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-0.575;ClippingRankSum=-0.021;DP=13977;ExcessHet=0.4576;FS=204.659;MLEAC=4;MLEAF=0.667;MQ=59.96;MQRankSum=-4.471;QD=34.54;ReadPosRankSum=0.207;SOR=5.956	GT:AD:DP:GQ:PL	0/0:5417,1:5418:99:0,16238,186152	1/1:0,4039:4039:99:139340,12147,0	1/1:1,4112:4113:99:142256,12338,0
MT	189	rs371543232	A	G	170933	.	AC=4;AF=0.667;AN=6;BaseQRankSum=3.014;ClippingRankSum=-0.01;DB;DP=7300;ExcessHet=0.4576;FS=126.051;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.01;QD=27.52;ReadPosRankSum=2.12;SOR=3.423	GT:AD:DP:GQ:PL	0/0:3069,0:3069:99:0,9284,133127	1/1:0,1721:1721:99:75953,5195,0	1/1:0,2204:2204:99:95018,6655,0
MT	195	rs2857291	T	C	159979	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-0.751;ClippingRankSum=-0.005;DB;DP=6293;ExcessHet=0.4576;FS=109.48;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.005;QD=34.79;ReadPosRankSum=2.083;SOR=2.995	GT:AD:DP:GQ:PL	0/0:2599,0:2599:99:0,8178,121032	1/1:0,1592:1592:99:73451,4949,0	1/1:0,1815:1815:99:86566,5885,0
MT	204	rs3135032	T	C	128466	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-6.588;ClippingRankSum=0;DB;DP=5182;ExcessHet=0.4576;FS=87.953;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=0;QD=32.74;ReadPosRankSum=7.907;SOR=2.255	GT:AD:DP:GQ:PL	0/0:2180,0:2180:99:0,6860,102449	1/1:0,1424:1424:99:66409,4455,0	1/1:0,1304:1304:99:62095,4160,0
MT	207	rs369669319	G	A	122208	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-9.258;ClippingRankSum=0;DB;DP=5067;ExcessHet=0.4576;FS=85.384;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=0;QD=28.38;ReadPosRankSum=7.499;SOR=2.1	GT:AD:DP:GQ:PL	0/0:2115,0:2115:99:0,6486,97099	1/1:0,1408:1408:99:64073,4304,0	1/1:0,1277:1277:99:58173,3904,0
MT	263	rs2853515	A	G	155184	.	AC=6;AF=1;AN=6;DB;DP=3763;ExcessHet=3.0103;FS=0;MLEAC=6;MLEAF=1;MQ=59.99;QD=31.62;SOR=1.803	GT:AD:DP:GQ:PL	1/1:0,1288:1288:99:51896,3929,0	1/1:0,1204:1204:99:55727,3751,0	1/1:0,1031:1031:99:47587,3194,0
MT	302	.	A	ACC	22823.1	.	AC=1;AF=0.167;AN=6;BaseQRankSum=-4.322;ClippingRankSum=0;DP=3315;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.167;MQ=59.99;MQRankSum=0;QD=27.04;ReadPosRankSum=0.436;SOR=0.233	GT:AD:DP:GQ:PL	0/1:157,687:844:99:22863,0,3831	0/0:1005,6:1011:99:0,2997,40313	0/0:800,3:803:99:0,2359,32031
MT	310	rs369786048	T	TC	144944	.	AC=6;AF=1;AN=6;BaseQRankSum=-0.232;ClippingRankSum=0;DB;DP=3730;ExcessHet=3.0103;FS=0;MLEAC=6;MLEAF=1;MQ=59.99;MQRankSum=0;QD=35.74;ReadPosRankSum=0.186;SOR=2.062	GT:AD:DP:GQ:PL	1/1:0,1035:1035:99:45452,3258,0	1/1:0,1411:1411:99:56001,4447,0	1/1:1,1090:1091:99:43526,3393,0
MT	477	rs41442247	T	C	71775.1	.	AC=2;AF=0.333;AN=6;BaseQRankSum=10.515;ClippingRankSum=-0;DB;DP=6218;ExcessHet=0.4576;FS=0;MLEAC=2;MLEAF=0.333;MQ=59.99;MQRankSum=-1.373;QD=33.65;ReadPosRankSum=-1.237;SOR=0.652	GT:AD:DP:GQ:PL	1/1:4,2129:2133:99:71813,6313,0	0/0:2266,1:2267:99:0,6783,76968	0/0:1725,0:1725:99:0,5198,58670
MT	709	rs2853517	G	A	134907	.	AC=4;AF=0.667;AN=6;BaseQRankSum=0.082;ClippingRankSum=-0;DB;DP=6675;ExcessHet=0.4576;FS=0.549;MLEAC=4;MLEAF=0.667;MQ=59.96;MQRankSum=-0.937;QD=33.73;ReadPosRankSum=-3.758;SOR=0.605	GT:AD:DP:GQ:PL	0/0:2494,0:2494:99:0,7486,84906	1/1:0,2186:2186:99:73800,6527,0	1/1:1,1813:1814:99:61145,5384,0
MT	750	rs2853518	A	G	263720	.	AC=6;AF=1;AN=6;DB;DP=6791;ExcessHet=3.0103;FS=0;MLEAC=6;MLEAF=1;MQ=59.96;QD=28.69;SOR=0.952	GT:AD:DP:GQ:PL	1/1:0,2757:2757:99:95517,8285,0	1/1:0,2392:2392:99:99668,7257,0	1/1:0,1621:1621:99:68561,4944,0
MT	879	.	T	C	12982.1	.	AC=1;AF=0.167;AN=6;BaseQRankSum=0.072;ClippingRankSum=-0.001;DP=7555;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.167;MQ=59.97;MQRankSum=0.595;QD=6.84;ReadPosRankSum=-0.892;SOR=0.637	GT:AD:DP:GQ:PL	0/0:2853,0:2853:99:0,8577,99352	0/0:2784,0:2784:99:0,8385,97374	0/1:1351,547:1898:99:13013,0,41295
MT	1243	rs28358572	T	C	133072	.	AC=4;AF=0.667;AN=6;BaseQRankSum=1.277;ClippingRankSum=-0.009;DB;DP=6544;ExcessHet=0.4576;FS=0.529;MLEAC=4;MLEAF=0.667;MQ=56.52;MQRankSum=-1.514;QD=34.54;ReadPosRankSum=-1.383;SOR=0.734	GT:AD:DP:GQ:PL	0/0:2674,1:2675:99:0,8015,92082	1/1:0,2198:2198:99:75833,6599,0	1/1:0,1655:1655:99:57277,4977,0
MT	1438	rs2001030	A	G	361231	.	AC=6;AF=1;AN=6;DB;DP=10389;ExcessHet=3.0103;FS=0;MLEAC=6;MLEAF=1;MQ=59.55;QD=34.84;SOR=0.765	GT:AD:DP:GQ:PL	1/1:0,3815:3815:99:132784,11475,0	1/1:0,3653:3653:99:127454,10989,0	1/1:0,2900:2900:99:101019,8735,0
MT	1824	.	T	C	92060.1	.	AC=2;AF=0.333;AN=6;BaseQRankSum=3.865;ClippingRankSum=-0.002;DP=6849;ExcessHet=0.4576;FS=0;MLEAC=2;MLEAF=0.333;MQ=59.97;MQRankSum=-2.685;QD=34.51;ReadPosRankSum=2.988;SOR=0.68	GT:AD:DP:GQ:PL	1/1:0,2668:2668:99:92098,8014,0	0/0:2409,0:2409:99:0,7229,82425	0/0:1752,0:1752:99:0,5262,60125
MT	2633	.	A	G	18823.1	.	AC=1;AF=0.167;AN=6;BaseQRankSum=2.98;ClippingRankSum=-0.001;DP=7233;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.167;MQ=59.99;MQRankSum=-0.972;QD=7.81;ReadPosRankSum=0.15;SOR=0.704	GT:AD:DP:GQ:PL	0/0:2535,0:2535:99:0,7596,86649	0/1:1648,761:2409:99:18854,0,49576	0/0:2269,0:2269:99:0,6817,78241
MT	2706	rs2854128	A	G	168629	.	AC=4;AF=0.667;AN=6;BaseQRankSum=7.196;ClippingRankSum=-0.002;DB;DP=8100;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-1.616;QD=34.65;ReadPosRankSum=-0.693;SOR=0.709	GT:AD:DP:GQ:PL	0/0:3200,0:3200:99:0,9590,109911	1/1:0,2847:2847:99:98532,8558,0	1/1:0,2020:2020:99:70135,6075,0
MT	3010	rs3928306	G	A	97056.1	.	AC=2;AF=0.333;AN=6;BaseQRankSum=0.588;ClippingRankSum=-0.001;DB;DP=6932;ExcessHet=0.4576;FS=1.119;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=-0.001;QD=34.16;ReadPosRankSum=0.778;SOR=0.63	GT:AD:DP:GQ:PL	1/1:0,2841:2841:99:97094,8518,0	0/0:2385,0:2385:99:0,7171,82143	0/0:1685,0:1685:99:0,5067,57965
MT	3505	rs28358585	A	G	139689	.	AC=4;AF=0.667;AN=6;BaseQRankSum=23.856;ClippingRankSum=-0.01;DB;DP=6709;ExcessHet=0.4576;FS=1.129;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.01;QD=34.69;ReadPosRankSum=4.12;SOR=0.765	GT:AD:DP:GQ:PL	0/0:2580,14:2594:99:0,7409,79067	1/1:0,2363:2363:99:81829,7100,0	1/1:0,1664:1664:99:57898,5007,0
MT	3784	.	T	C	74911.1	.	AC=1;AF=0.167;AN=6;BaseQRankSum=8.222;ClippingRankSum=-0.001;DP=7466;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=-0.001;QD=25.51;ReadPosRankSum=8.984;SOR=0.643	GT:AD:DP:GQ:PL	0/1:480,2456:2936:99:74942,0,7261	0/0:2504,0:2504:99:0,7501,84964	0/0:1991,0:1991:99:0,5980,67446
MT	4769	rs3021086	A	G	250394	.	AC=6;AF=1;AN=6;DB;DP=7354;ExcessHet=3.0103;FS=0;MLEAC=6;MLEAF=1;MQ=38.53;QD=34.09;SOR=0.908	GT:AD:DP:GQ:PL	1/1:0,2689:2689:99:91629,8095,0	1/1:0,2549:2549:99:87520,7686,0	1/1:0,2108:2108:99:71271,6343,0
MT	5046	.	G	A	141138	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-0.013;ClippingRankSum=-0.011;DP=7024;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=58.01;MQRankSum=-1.451;QD=34.2;ReadPosRankSum=-1.049;SOR=0.71	GT:AD:DP:GQ:PL	0/0:2876,2:2878:99:0,8603,98489	1/1:0,2466:2466:99:84329,7395,0	1/1:0,1661:1661:99:56847,4982,0
MT	5460	rs3021088	G	A	163621	.	AC=4;AF=0.667;AN=6;BaseQRankSum=8.973;ClippingRankSum=-0.014;DB;DP=7661;ExcessHet=0.4576;FS=0.533;MLEAC=4;MLEAF=0.667;MQ=59.97;MQRankSum=2.211;QD=34.6;ReadPosRankSum=-4.336;SOR=0.639	GT:AD:DP:GQ:PL	0/0:2905,2:2907:99:0,8649,98530	1/1:0,2759:2759:99:95680,8294,0	1/1:2,1968:1970:99:67979,5859,0
MT	7028	rs2015062	C	T	141599	.	AC=4;AF=0.667;AN=6;BaseQRankSum=4.572;ClippingRankSum=-0.001;DB;DP=6737;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=49.86;MQRankSum=3.057;QD=34.13;ReadPosRankSum=-3.721;SOR=0.674	GT:AD:DP:GQ:PL	0/0:2577,3:2580:99:0,7648,87327	1/1:2,2201:2203:99:75290,6579,0	1/1:1,1945:1946:99:66347,5809,0
MT	7864	.	C	T	208656	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-9.133;ClippingRankSum=-0.022;DP=9838;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=59.36;MQRankSum=-5.235;QD=33.59;ReadPosRankSum=-3.037;SOR=0.676	GT:AD:DP:GQ:PL	0/0:3588,1:3589:99:0,10779,123905	1/1:0,3465:3465:99:116339,10336,0	1/1:0,2746:2746:99:92355,8209,0
MT	8170	.	A	G	140467	.	AC=4;AF=0.667;AN=6;BaseQRankSum=2.197;ClippingRankSum=-0;DP=6117;ExcessHet=0.4576;FS=1.859;MLEAC=4;MLEAF=0.667;MQ=59.96;MQRankSum=3.961;QD=34.85;ReadPosRankSum=-3.38;SOR=0.845	GT:AD:DP:GQ:PL	0/0:2051,1:2052:99:0,6099,69511	1/1:0,2257:2257:99:78536,6792,0	1/1:0,1774:1774:99:61969,5349,0
MT	8251	rs3021089	G	A	136520	.	AC=4;AF=0.667;AN=6;BaseQRankSum=3.941;ClippingRankSum=-0.009;DB;DP=6322;ExcessHet=0.4576;FS=2.552;MLEAC=4;MLEAF=0.667;MQ=53.44;MQRankSum=3.131;QD=34.63;ReadPosRankSum=-2.517;SOR=0.903	GT:AD:DP:GQ:PL	0/0:2360,0:2360:99:0,7086,80769	1/1:0,2317:2317:99:80192,6966,0	1/1:1,1624:1625:99:56366,4872,0
MT	8860	rs2001031	A	G	293052	.	AC=6;AF=1;AN=6;DB;DP=8612;ExcessHet=3.0103;FS=0;MLEAC=6;MLEAF=1;MQ=36.86;QD=34.05;SOR=0.722	GT:AD:DP:GQ:PL	1/1:0,3278:3278:99:111938,9859,0	1/1:0,3088:3088:99:105297,9289,0	1/1:0,2241:2241:99:75843,6755,0
MT	8994	rs28358887	G	A	145674	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-5.687;ClippingRankSum=-0.001;DB;DP=7101;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=51.96;MQRankSum=-5.832;QD=33.99;ReadPosRankSum=-6.301;SOR=0.69	GT:AD:DP:GQ:PL	0/0:2793,0:2793:99:0,8571,124921	1/1:0,2368:2368:99:80498,7100,0	1/1:1,1917:1918:99:65214,5748,0
MT	9007	.	A	G	102350	.	AC=2;AF=0.333;AN=6;BaseQRankSum=3.474;ClippingRankSum=-0.001;DP=7154;ExcessHet=0.4576;FS=0;MLEAC=2;MLEAF=0.333;MQ=54.08;MQRankSum=-1.247;QD=34.59;ReadPosRankSum=2.258;SOR=0.697	GT:AD:DP:GQ:PL	1/1:0,2959:2959:99:102388,8899,0	0/0:2442,0:2442:99:0,7470,106684	0/0:1735,0:1735:99:0,5457,77467
MT	9150	.	A	G	107647	.	AC=2;AF=0.333;AN=6;BaseQRankSum=-1.302;ClippingRankSum=-0.007;DP=9489;ExcessHet=0.4576;FS=0;MLEAC=2;MLEAF=0.333;MQ=55.22;MQRankSum=-2.786;QD=34.03;ReadPosRankSum=4.955;SOR=0.699	GT:AD:DP:GQ:PL	1/1:0,3163:3163:99:107685,9502,0	0/0:3538,0:3538:99:0,10633,121609	0/0:2767,0:2767:99:0,8321,94924
MT	9380	.	G	A	114009	.	AC=2;AF=0.333;AN=6;BaseQRankSum=15.183;ClippingRankSum=-0.008;DP=9110;ExcessHet=0.4576;FS=0;MLEAC=2;MLEAF=0.333;MQ=55.3;MQRankSum=-2.132;QD=34.33;ReadPosRankSum=6.04;SOR=0.731	GT:AD:DP:GQ:PL	1/1:1,3320:3321:99:114047,9929,0	0/0:3222,0:3222:99:0,9596,104739	0/0:2547,0:2547:99:0,7657,86810
MT	10097	.	A	G	10814.1	.	AC=1;AF=0.167;AN=6;BaseQRankSum=2.899;ClippingRankSum=-0.001;DP=6730;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=-0.001;QD=4.94;ReadPosRankSum=0.898;SOR=0.663	GT:AD:DP:GQ:PL	0/0:2660,0:2660:99:0,7994,91201	0/1:1680,508:2188:99:10845,0,50969	0/0:1851,0:1851:99:0,5557,63188
MT	11204	rs201803443	T	C	183666	.	AC=4;AF=0.667;AN=6;BaseQRankSum=6.514;ClippingRankSum=-0.015;DB;DP=8553;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=59.96;MQRankSum=2.593;QD=34.39;ReadPosRankSum=-6.507;SOR=0.665	GT:AD:DP:GQ:PL	0/0:3168,5:3173:99:0,9411,106928	1/1:0,2922:2922:99:100296,8776,0	1/1:0,2418:2418:99:83408,7267,0
MT	11674	rs28358286	C	T	167026	.	AC=4;AF=0.667;AN=6;BaseQRankSum=2.538;ClippingRankSum=-0.016;DB;DP=7754;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=58.56;MQRankSum=-26.225;QD=34.47;ReadPosRankSum=-6.727;SOR=0.689	GT:AD:DP:GQ:PL	0/0:2890,0:2890:99:0,8678,99225	1/1:0,2666:2666:99:91850,8010,0	1/1:1,2179:2180:99:75214,6545,0
MT	11719	rs2853495	G	A	181704	.	AC=4;AF=0.667;AN=6;BaseQRankSum=2.012;ClippingRankSum=-0.016;DB;DP=8621;ExcessHet=0.4576;FS=1.122;MLEAC=4;MLEAF=0.667;MQ=58.72;MQRankSum=-26.852;QD=34.58;ReadPosRankSum=-2.878;SOR=0.775	GT:AD:DP:GQ:PL	0/0:3339,2:3341:99:0,9993,114829	1/1:0,3052:3052:99:105503,9166,0	1/1:0,2203:2203:99:76239,6625,0
MT	11947	rs28359168	A	G	138146	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-6.069;ClippingRankSum=-0.011;DB;DP=6674;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=59.99;MQRankSum=1.198;QD=33.88;ReadPosRankSum=-3.658;SOR=0.672	GT:AD:DP:GQ:PL	0/0:2579,2:2581:99:0,7727,88892	1/1:0,2273:2273:99:77242,6825,0	1/1:0,1804:1804:99:60942,5416,0
MT	12414	rs193302950	T	C	147603	.	AC=4;AF=0.667;AN=6;BaseQRankSum=10.932;ClippingRankSum=-0.001;DB;DP=7160;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.001;QD=34.49;ReadPosRankSum=0.393;SOR=0.65	GT:AD:DP:GQ:PL	0/0:2852,3:2855:99:0,8482,95556	1/1:1,2545:2546:99:87714,7616,0	1/1:0,1733:1733:99:59927,5208,0
MT	12648	.	A	G	117695	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-0.891;ClippingRankSum=0.002;DP=5272;ExcessHet=0.4576;FS=0.548;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=0.002;QD=34.16;ReadPosRankSum=-3.778;SOR=0.739	GT:AD:DP:GQ:PL	0/0:1812,1:1813:99:0,5398,61087	1/1:2,1662:1664:99:56988,4945,0	1/1:4,1777:1781:99:60745,5214,0
MT	12705	rs193302956	C	T	129264	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-1.576;ClippingRankSum=-0.008;DB;DP=6157;ExcessHet=0.4576;FS=0.531;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.008;QD=34.38;ReadPosRankSum=0.001;SOR=0.709	GT:AD:DP:GQ:PL	0/0:2359,10:2369:99:0,6679,80813	1/1:1,2137:2138:99:73546,6407,0	1/1:1,1621:1622:99:55756,4857,0
MT	13406	.	G	A	18935.1	.	AC=1;AF=0.167;AN=6;BaseQRankSum=4.892;ClippingRankSum=-0.001;DP=6741;ExcessHet=3.0103;FS=0.853;MLEAC=1;MLEAF=0.167;MQ=59.93;MQRankSum=1.557;QD=9.68;ReadPosRankSum=-3.763;SOR=0.717	GT:AD:DP:GQ:PL	0/0:2539,1:2540:99:0,7611,88829	0/0:2216,0:2216:99:0,6672,76749	0/1:1224,733:1957:99:18966,0,36219
MT	13611	.	A	G	226523	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-0.715;ClippingRankSum=-0.018;DP=10456;ExcessHet=0.4576;FS=0.541;MLEAC=4;MLEAF=0.667;MQ=59.95;MQRankSum=3.806;QD=34.57;ReadPosRankSum=-3.084;SOR=0.749	GT:AD:DP:GQ:PL	0/0:3838,2:3840:99:0,11470,131432	1/1:0,3717:3717:99:128767,11180,0	1/1:1,2834:2835:99:97794,8490,0
MT	13928	rs28359184	G	C	158255	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-2.077;ClippingRankSum=-0.001;DB;DP=7572;ExcessHet=0.4576;FS=0.537;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.001;QD=34.55;ReadPosRankSum=0.177;SOR=0.614	GT:AD:DP:GQ:PL	0/0:2947,0:2947:99:0,8798,100755	1/1:0,2700:2700:99:93028,8117,0	1/1:0,1880:1880:99:65265,5652,0
MT	14148	rs28357668	A	G	163476	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-0.068;ClippingRankSum=-0.002;DB;DP=7865;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=59.96;MQRankSum=3.807;QD=34.19;ReadPosRankSum=1.224;SOR=0.702	GT:AD:DP:GQ:PL	0/0:3019,2:3021:99:0,9046,102891	1/1:0,2820:2820:99:96517,8442,0	1/1:0,1962:1962:99:66997,5890,0
MT	14766	rs527236041	C	T	184246	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-4.916;ClippingRankSum=-0.016;DB;DP=8840;ExcessHet=0.4576;FS=1.797;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.93;QD=33.68;ReadPosRankSum=-8.259;SOR=0.565	GT:AD:DP:GQ:PL	0/0:3318,3:3321:99:0,9897,113210	1/1:2,3111:3113:99:104758,9287,0	1/1:3,2355:2358:99:79526,6992,0
MT	15326	rs2853508	A	G	351443	.	AC=6;AF=1;AN=6;DB;DP=9986;ExcessHet=3.0103;FS=0;MLEAC=6;MLEAF=1;MQ=60;QD=23.43;SOR=0.788	GT:AD:DP:GQ:PL	1/1:0,3716:3716:99:131483,11200,0	1/1:0,3560:3560:99:125277,10713,0	1/1:0,2690:2690:99:94709,8122,0
MT	15884	.	G	C	203141	.	AC=4;AF=0.667;AN=6;BaseQRankSum=1.841;ClippingRankSum=-0.02;DP=9526;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.02;QD=34.42;ReadPosRankSum=-6.501;SOR=0.721	GT:AD:DP:GQ:PL	0/0:3595,1:3596:99:0,10754,123245	1/1:0,3167:3167:99:109155,9521,0	1/1:1,2733:2734:99:94024,8195,0
MT	16184	rs34100702	C	T	118028	.	AC=4;AF=0.667;AN=6;BaseQRankSum=3.32;ClippingRankSum=0;DB;DP=4885;ExcessHet=0.4576;FS=3.599;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=0;QD=34.24;ReadPosRankSum=2.363;SOR=0.93	GT:AD:DP:GQ:PL	0/0:1406,1:1407:99:0,4183,47484	1/1:0,1969:1969:99:67640,5881,0	1/1:0,1478:1478:99:50426,4408,0
MT	16223	rs2853513	C	T	120350	.	AC=4;AF=0.667;AN=6;BaseQRankSum=0.452;ClippingRankSum=-0.001;DB;DP=4936;ExcessHet=0.4576;FS=8.04;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.001;QD=34.48;ReadPosRankSum=0.914;SOR=1.051	GT:AD:DP:GQ:PL	0/0:1405,1:1406:99:0,4181,48090	1/1:0,2018:2018:99:69507,6063,0	1/1:0,1472:1472:99:50881,4420,0
MT	16263	.	T	C	50770.1	.	AC=2;AF=0.333;AN=6;BaseQRankSum=-1.81;ClippingRankSum=0;DP=5017;ExcessHet=0.4576;FS=18.084;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=34.35;ReadPosRankSum=-1.303;SOR=0.23	GT:AD:DP:GQ:PL	1/1:2,1476:1478:99:50817,4422,0	0/0:1994,0:1994:99:0,5989,69016	0/0:1475,0:1475:99:0,4439,51221
MT	16292	rs144417390	C	T	113132	.	AC=4;AF=0.667;AN=6;BaseQRankSum=-7.684;ClippingRankSum=-0.001;DB;DP=5092;ExcessHet=0.4576;FS=26.574;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.001;QD=33.37;ReadPosRankSum=4.375;SOR=2.115	GT:AD:DP:GQ:PL	0/0:1652,0:1652:99:0,4962,57207	1/1:1,1913:1914:99:63339,5702,0	1/1:0,1476:1476:99:49831,4419,0
MT	16519	rs3937033	T	C	263844	.	AC=6;AF=1;AN=6;DB;DP=7636;ExcessHet=3.0103;FS=0;MLEAC=6;MLEAF=1;MQ=60;QD=34.73;SOR=3.902	GT:AD:DP:GQ:PL	1/1:0,1759:1759:99:61243,5289,0	1/1:0,4094:4094:99:142289,12314,0	1/1:0,1744:1744:99:60338,5251,0