##fileformat=VCFv4.1
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
##FILTER=<ID=filter,Description="(AB ?: 0) > 0.75 || QUAL < 50.0 || DP > 360 || SB > -0.1 || MQ0>=4">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##GATKCommandLine=<ID=VariantFiltration,CommandLineOptions="analysis_type=VariantFiltration input_file=[] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/srv/gs1/projects/cherry/sacCer3/sacCer3.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false 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 num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/srv/gs1/projects/cherry/giltae/strains/hugeseq/BY4741/chrI.indel.gatk.vcf) mask=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub filterExpression=[(AB ?: 0) > 0.75 || QUAL < 50.0 || DP > 360 || SB > -0.1 || MQ0>=4] filterName=[filter] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=10 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Tue Jan 14 23:15:55 PST 2014",Epoch=1389770155184,Version=2.8-1-g932cd3a>
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/srv/gs1/projects/cherry/giltae/strains/hugeseq/BY4741/chrI.recal.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/srv/gs1/projects/cherry/sacCer3/sacCer3.fa 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 BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=LENIENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 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 generateShadowBCF=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT pcr_error_rate=1.0E-4 noSLOD=false annotateNDA=false min_base_quality_score=17 max_deletion_fraction=0.05 cap_max_alternate_alleles_for_indels=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 noBandedIndel=false indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.001 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=3 dbsnp=(RodBinding name=dbsnp source=/srv/gs1/projects/cherry/giltae/hugeseq_data/snp.d/chrI_SNPs.vcf) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null metrics_file=null annotation=[DepthOfCoverage, MappingQualityZero] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig=<ID=chrI,length=230218>
##contig=<ID=chrII,length=813184>
##contig=<ID=chrIII,length=316620>
##contig=<ID=chrIV,length=1531933>
##contig=<ID=chrV,length=576874>
##contig=<ID=chrVI,length=270161>
##contig=<ID=chrVII,length=1090940>
##contig=<ID=chrVIII,length=562643>
##contig=<ID=chrIX,length=439888>
##contig=<ID=chrX,length=745751>
##contig=<ID=chrXI,length=666816>
##contig=<ID=chrXII,length=1078177>
##contig=<ID=chrXIII,length=924431>
##contig=<ID=chrXIV,length=784333>
##contig=<ID=chrXV,length=1091291>
##contig=<ID=chrXVI,length=948066>
##contig=<ID=chrM,length=85779>
##reference=file:///srv/gs1/projects/cherry/sacCer3/sacCer3.fa
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	BY4741
chrI	6736	.	C	CAA	745.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.056;DP=91;FS=7.482;HaplotypeScore=50.5936;MLEAC=2;MLEAF=1.00;MQ=61.60;MQ0=0;MQRankSum=1.062;QD=8.20;RPA=19,21;RU=A;ReadPosRankSum=0.950;SB=-1.590e+02;STR	GT:AD:DP:GQ:PL	1/1:57,28:91:54:788,54,0
chrI	19971	.	C	CCT	2431.96	filter	AC=2;AF=1.00;AN=2;DP=104;FS=0.000;HaplotypeScore=4.6265;MLEAC=2;MLEAF=1.00;MQ=23.54;MQ0=29;QD=23.38;SB=-9.310e+02	GT:AD:DP:GQ:PL	1/1:0,101:49:99:2474,141,0
chrI	101281	.	C	CA	906.50	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.815;DP=147;FS=3.020;HaplotypeScore=281.3011;MLEAC=2;MLEAF=1.00;MQ=59.77;MQ0=0;MQRankSum=2.116;QD=6.17;RPA=24,25;RU=A;ReadPosRankSum=-2.398;SB=-4.738e+02;STR	GT:AD:DP:GQ:PL	1/1:102,45:147:2:945,2,0
chrI	126880	.	C	CT,CTT	6652	PASS	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.086;DP=232;FS=0.000;HaplotypeScore=187.2463;MLEAC=1,1;MLEAF=0.500,0.500;MQ=65.04;MQ0=0;MQRankSum=1.096;QD=28.67;RPA=15,16,17;RU=T;ReadPosRankSum=-0.901;SB=-1.415e+03;STR	GT:AD:DP:GQ:PL	1/2:26,13,184:232:99:6652,3506,2984,678,0,174
chrI	183387	.	AC	A	4777	PASS	AC=2;AF=1.00;AN=2;DP=145;FS=0.000;HaplotypeScore=26.4801;MLEAC=2;MLEAF=1.00;MQ=36.23;MQ0=3;QD=32.94;RPA=2,1;RU=C;SB=-1.844e+03;STR	GT:AD:DP:GQ:PL	1/1:0,145:116:99:4777,349,0
chrI	206176	.	CG	C	2516.96	filter	AC=2;AF=1.00;AN=2;BaseQRankSum=1.567;DP=74;FS=0.000;HaplotypeScore=426.4678;MLEAC=2;MLEAF=1.00;MQ=29.58;MQ0=6;MQRankSum=1.292;QD=34.01;ReadPosRankSum=1.567;SB=-1.098e+03	GT:AD:DP:GQ:PL	1/1:32,42:63:99:2559,180,0
chrI	206179	.	A	AC	2619.96	filter	AC=2;AF=1.00;AN=2;BaseQRankSum=1.251;DP=88;FS=0.000;HaplotypeScore=448.7508;MLEAC=2;MLEAF=1.00;MQ=28.61;MQ0=10;MQRankSum=0.962;QD=29.77;RPA=1,2;RU=C;ReadPosRankSum=0.770;SB=-1.029e+03;STR	GT:AD:DP:GQ:PL	1/1:46,42:72:99:2662,207,0
chrII	7912	.	GA	G	715.96	filter	AC=2;AF=1.00;AN=2;DP=56;FS=0.000;HaplotypeScore=9.8849;MLEAC=2;MLEAF=1.00;MQ=22.67;MQ0=9;QD=12.78;RPA=3,2;RU=A;SB=-3.720e+02;STR	GT:AD:DP:GQ:PL	1/1:13,42:32:57:758,57,0
chrII	88484	.	GGAGAA	G	13007	PASS	AC=2;AF=1.00;AN=2;DP=183;FS=0.000;HaplotypeScore=32.3064;MLEAC=2;MLEAF=1.00;MQ=49.34;MQ0=0;QD=71.08;RPA=2,1;RU=GAGAA;SB=-2.985e+03;STR	GT:AD:DP:GQ:PL	1/1:13,169:183:99:13007,512,0
chrII	167978	.	C	CA	1286.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.895;DP=111;FS=7.550;HaplotypeScore=79.6882;MLEAC=1;MLEAF=0.500;MQ=61.70;MQ0=0;MQRankSum=2.513;QD=11.59;RPA=16,17;RU=A;ReadPosRankSum=-1.514;SB=-7.900e+01;STR	GT:AD:DP:GQ:PL	0/1:47,57:111:99:1326,0,143
chrII	221288	.	AGT	A	2827.96	PASS	AC=2;AF=1.00;AN=2;DP=68;FS=0.000;HaplotypeScore=6.0641;MLEAC=2;MLEAF=1.00;MQ=35.21;MQ0=0;QD=41.59;RPA=2,1;RU=GT;SB=-5.040e+02;STR	GT:AD:DP:GQ:PL	1/1:1,67:65:99:2870,193,0
chrII	263158	.	CG	C	478.96	PASS	AC=2;AF=1.00;AN=2;DP=13;FS=0.000;HaplotypeScore=127.8144;MLEAC=2;MLEAF=1.00;MQ=35.32;MQ0=0;QD=36.84;RPA=2,1;RU=G;SB=-4.400e+01;STR	GT:AD:DP:GQ:PL	1/1:0,12:13:36:521,36,0
chrII	263168	.	CG	C	752.96	PASS	AC=2;AF=1.00;AN=2;DP=17;FS=0.000;HaplotypeScore=119.5434;MLEAC=2;MLEAF=1.00;MQ=37.39;MQ0=0;QD=44.29;SB=-2.370e+02	GT:AD:DP:GQ:PL	1/1:0,17:17:51:795,51,0
chrII	383176	.	C	CG	6157	PASS	AC=2;AF=1.00;AN=2;DP=155;FS=0.000;HaplotypeScore=46.2567;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=39.72;RPA=2,3;RU=G;SB=-1.758e+03;STR	GT:AD:DP:GQ:PL	1/1:4,146:155:99:6157,451,0
chrII	389425	.	T	TTG	6521	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.474;DP=134;FS=0.000;HaplotypeScore=951.4585;MLEAC=2;MLEAF=1.00;MQ=50.44;MQ0=0;MQRankSum=-0.724;QD=48.66;ReadPosRankSum=1.706;SB=-2.702e+03	GT:AD:DP:GQ:PL	1/1:13,5:134:99:6521,387,0
chrII	389429	.	CG	C	4590	PASS	AC=2;AF=1.00;AN=2;DP=130;FS=0.000;HaplotypeScore=1091.2999;MLEAC=2;MLEAF=1.00;MQ=50.75;MQ0=0;QD=35.31;SB=-2.008e+03	GT:AD:DP:GQ:PL	1/1:14,113:130:99:4590,373,0
chrII	723663	.	C	CAA,CA	2417.94	PASS	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.455;DP=145;FS=5.487;HaplotypeScore=147.6052;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.10;MQ0=0;MQRankSum=2.286;QD=16.68;RPA=15,17,16;RU=A;ReadPosRankSum=0.602;SB=-6.809e+02;STR	GT:AD:DP:GQ:PL	1/2:44,10,89:145:99:2496,1394,1621,109,0,108
chrII	746362	.	CATCTGCA	C	13893	PASS	AC=2;AF=1.00;AN=2;DP=162;FS=0.000;HaplotypeScore=25.5430;MLEAC=2;MLEAF=1.00;MQ=59.75;MQ0=0;QD=85.76;RPA=2,1;RU=ATCTGCA;SB=-5.179e+03;STR	GT:AD:DP:GQ:PL	1/1:13,148:160:99:13893,446,0
chrII	809794	.	AT	A	865.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=136;FS=0.000;HaplotypeScore=95.4853;MLEAC=1;MLEAF=0.500;MQ=45.96;MQ0=14;MQRankSum=0.456;QD=6.37;RPA=19,18;RU=T;ReadPosRankSum=1.292;SB=-3.470e+02;STR	GT:AD:DP:GQ:PL	0/1:91,36:115:99:905,0,266
chrIII	27658	.	T	TAA	845.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.891;DP=151;FS=24.962;HaplotypeScore=186.5944;MLEAC=1;MLEAF=0.500;MQ=62.29;MQ0=0;MQRankSum=5.105;QD=5.60;RPA=23,25;RU=A;ReadPosRankSum=1.886;SB=-1.880e+02;STR	GT:AD:DP:GQ:PL	0/1:104,41:151:99:885,0,178
chrIII	162712	.	TA	T	3586	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=1.303;DP=129;FS=4.403;HaplotypeScore=491.3365;MLEAC=2;MLEAF=1.00;MQ=59.74;MQ0=0;MQRankSum=0.720;QD=27.80;RPA=10,9;RU=A;ReadPosRankSum=1.088;SB=-1.260e+03;STR	GT:AD:DP:GQ:PL	1/1:16,113:129:99:3586,306,0
chrIII	163163	.	G	GA	5036	PASS	AC=2;AF=1.00;AN=2;DP=176;FS=0.000;HaplotypeScore=490.9302;MLEAC=2;MLEAF=1.00;MQ=59.61;MQ0=0;QD=28.61;RPA=9,10;RU=A;SB=-2.286e+03;STR	GT:AD:DP:GQ:PL	1/1:21,144:176:99:5036,451,0
chrIII	163192	.	A	AT	5647	PASS	AC=2;AF=1.00;AN=2;DP=150;FS=0.000;HaplotypeScore=431.2530;MLEAC=2;MLEAF=1.00;MQ=59.89;MQ0=0;QD=37.65;RPA=3,4;RU=T;SB=-2.009e+03;STR	GT:AD:DP:GQ:PL	1/1:3,147:150:99:5647,442,0
chrIII	231005	.	C	CT	1108.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.507;DP=136;FS=2.304;HaplotypeScore=347.8774;MLEAC=1;MLEAF=0.500;MQ=61.96;MQ0=0;MQRankSum=2.331;QD=8.15;RPA=19,20;RU=T;ReadPosRankSum=-0.439;SB=-3.240e+02;STR	GT:AD:DP:GQ:PL	0/1:64,58:136:99:1148,0,492
chrIV	169891	.	TA	T	451.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;DP=166;FS=0.000;HaplotypeScore=649.4976;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=0;MQRankSum=-1.070;QD=2.72;RPA=18,17;RU=A;ReadPosRankSum=-0.639;SB=-8.144e-04;STR	GT:AD:DP:GQ:PL	0/1:121,21:166:99:491,0,2336
chrIV	344004	.	G	GTA	2159.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.397;DP=174;FS=3.277;HaplotypeScore=88.9943;MLEAC=1;MLEAF=0.500;MQ=60.46;MQ0=0;MQRankSum=1.365;QD=12.41;RPA=13,14;RU=TA;ReadPosRankSum=-0.653;SB=-1.001e+03;STR	GT:AD:DP:GQ:PL	0/1:106,54:174:99:2199,0,789
chrIV	403511	.	G	GT	4666	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.064;DP=147;FS=0.000;HaplotypeScore=42.0008;MLEAC=2;MLEAF=1.00;MQ=60.13;MQ0=0;MQRankSum=0.593;QD=31.74;RPA=9,10;RU=T;ReadPosRankSum=0.907;SB=-1.974e+03;STR	GT:AD:DP:GQ:PL	1/1:4,136:146:99:4666,324,0
chrIV	548546	.	G	GT	1337.50	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.652;DP=118;FS=40.302;HaplotypeScore=171.7737;MLEAC=2;MLEAF=1.00;MQ=61.64;MQ0=0;MQRankSum=2.364;QD=11.33;RPA=19,20;RU=T;ReadPosRankSum=-0.577;SB=-4.705e+02;STR	GT:AD:DP:GQ:PL	1/1:49,60:118:2:1376,2,0
chrIV	688062	.	C	CT,CTT	4200	PASS	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.558;DP=143;FS=0.000;HaplotypeScore=118.6367;MLEAC=1,1;MLEAF=0.500,0.500;MQ=62.04;MQ0=0;MQRankSum=-0.264;QD=29.37;RPA=14,15,16;RU=T;ReadPosRankSum=-0.675;SB=-2.066e+03;STR	GT:AD:DP:GQ:PL	1/2:30,13,96:143:99:4200,2637,2342,465,0,180
chrIV	817531	.	T	TA	4282	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.999;DP=153;FS=1.669;HaplotypeScore=43.7262;MLEAC=2;MLEAF=1.00;MQ=60.56;MQ0=0;MQRankSum=1.216;QD=27.99;RPA=10,11;RU=A;ReadPosRankSum=0.120;SB=-2.037e+03;STR	GT:AD:DP:GQ:PL	1/1:19,129:153:99:4282,246,0
chrIV	1150910	.	A	AG	6107	PASS	AC=2;AF=1.00;AN=2;DP=158;FS=0.000;HaplotypeScore=42.7491;MLEAC=2;MLEAF=1.00;MQ=57.06;MQ0=0;QD=38.65;RPA=2,3;RU=G;SB=-2.703e+03;STR	GT:AD:DP:GQ:PL	1/1:6,152:152:99:6107,439,0
chrIV	1305680	.	TG	T	5342	PASS	AC=2;AF=1.00;AN=2;DP=142;FS=0.000;HaplotypeScore=27.3608;MLEAC=2;MLEAF=1.00;MQ=60.52;MQ0=0;QD=37.62;RPA=2,1;RU=G;SB=-1.157e+03;STR	GT:AD:DP:GQ:PL	1/1:0,129:142:99:5342,388,0
chrIV	1515034	.	TA	T	4568	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.086;DP=156;FS=0.000;HaplotypeScore=41.6527;MLEAC=2;MLEAF=1.00;MQ=59.60;MQ0=0;MQRankSum=-1.221;QD=29.28;RPA=11,10;RU=A;ReadPosRankSum=1.069;SB=-1.648e+03;STR	GT:AD:DP:GQ:PL	1/1:11,143:156:99:4568,394,0
chrIV	1518948	.	G	GT	4111	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.683;DP=176;FS=16.414;HaplotypeScore=93.1269;MLEAC=2;MLEAF=1.00;MQ=60.40;MQ0=1;MQRankSum=0.794;QD=23.36;RPA=13,14;RU=T;ReadPosRankSum=0.824;SB=-1.160e+03;STR	GT:AD:DP:GQ:PL	1/1:33,133:175:77:4111,77,0
chrIV	1525376	.	TG	T	3397	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.905;DP=133;FS=18.800;HaplotypeScore=4703.3765;MLEAC=1;MLEAF=0.500;MQ=28.10;MQ0=2;MQRankSum=0.774;QD=25.54;RPA=3,2;RU=G;ReadPosRankSum=2.645;SB=-2.120e+02;STR	GT:AD:DP:GQ:PL	0/1:49,80:123:28:3397,0,28
chrIV	1525391	.	GT	G	2260.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=7.605;DP=143;FS=106.237;HaplotypeScore=3895.3923;MLEAC=1;MLEAF=0.500;MQ=27.01;MQ0=7;MQRankSum=-1.999;QD=15.81;ReadPosRankSum=4.272;SB=-8.144e-04	GT:AD:DP:GQ:PL	0/1:87,47:118:99:2300,0,1037
chrIV	1525404	.	GGGT	G	868.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=5.451;DP=146;FS=71.871;HaplotypeScore=3221.9015;MLEAC=1;MLEAF=0.500;MQ=26.86;MQ0=8;MQRankSum=-2.677;QD=5.95;ReadPosRankSum=1.927;SB=-7.697e+01	GT:AD:DP:GQ:PL	0/1:113,12:118:99:908,0,2000
chrIX	39373	.	T	TA	4872	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.599;DP=184;FS=0.000;HaplotypeScore=70.8283;MLEAC=2;MLEAF=1.00;MQ=59.30;MQ0=0;MQRankSum=-0.882;QD=26.48;RPA=11,12;RU=A;ReadPosRankSum=-0.940;SB=-1.340e+03;STR	GT:AD:DP:GQ:PL	1/1:23,151:184:99:4872,321,0
chrIX	57277	.	C	CA	1472.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.646;DP=115;FS=3.246;HaplotypeScore=120.4078;MLEAC=1;MLEAF=0.500;MQ=63.88;MQ0=0;MQRankSum=3.585;QD=12.81;RPA=16,17;RU=A;ReadPosRankSum=-3.176;SB=-5.900e+02;STR	GT:AD:DP:GQ:PL	0/1:40,71:115:89:1512,0,89
chrIX	105433	.	A	AAAT	4594	PASS	AC=2;AF=1.00;AN=2;DP=87;FS=0.000;HaplotypeScore=22.7751;MLEAC=2;MLEAF=1.00;MQ=60.79;MQ0=0;QD=52.80;RPA=3,4;RU=AAT;SB=-2.231e+03;STR	GT:AD:DP:GQ:PL	1/1:5,82:87:99:4594,250,0
chrIX	241032	.	G	GA	838.01	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.439;DP=99;FS=4.851;HaplotypeScore=234.1030;MLEAC=1;MLEAF=0.500;MQ=64.00;MQ0=0;MQRankSum=5.015;QD=8.46;RPA=21,22;RU=A;ReadPosRankSum=0.080;SB=-6.653e+01;STR	GT:AD:DP:GQ:PL	0/1:45,50:99:17:877,0,17
chrIX	245961	.	TC	T	572.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=6.215;DP=128;FS=268.302;HaplotypeScore=88.7502;MLEAC=1;MLEAF=0.500;MQ=60.05;MQ0=0;MQRankSum=4.502;QD=4.48;ReadPosRankSum=-5.080;SB=-3.011e+00	GT:AD:DP:GQ:PL	0/1:91,36:128:99:612,0,2660
chrIX	254003	.	TA	T	2713.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.526;DP=165;FS=0.000;HaplotypeScore=88.3956;MLEAC=2;MLEAF=1.00;MQ=60.38;MQ0=0;MQRankSum=-0.552;QD=16.45;RPA=15,14;RU=A;ReadPosRankSum=1.655;SB=-9.090e+02;STR	GT:AD:DP:GQ:PL	1/1:58,91:165:99:2756,221,0
chrIX	339225	.	C	CTT	499.07	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.138;DP=76;FS=0.000;HaplotypeScore=167.0170;MLEAC=2;MLEAF=1.00;MQ=60.98;MQ0=0;MQRankSum=2.565;QD=6.57;RPA=25,27;RU=T;ReadPosRankSum=-0.083;SB=-1.077e+02;STR	GT:AD:DP:GQ:PL	1/1:50,23:75:19:541,19,0
chrM	20345	.	GA	G	7950	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.718;DP=248;DS;FS=0.000;HaplotypeScore=77.2060;MLEAC=2;MLEAF=1.00;MQ=59.46;MQ0=0;MQRankSum=1.704;QD=32.06;RPA=3,2;RU=A;ReadPosRankSum=0.517;SB=-3.292e+03;STR	GT:AD:DP:GQ:PL	1/1:9,239:248:99:7950,719,0
chrM	33618	.	T	TTC	7976	PASS	AC=2;AF=1.00;AN=2;DP=162;FS=0.000;HaplotypeScore=45.0786;MLEAC=2;MLEAF=1.00;MQ=58.12;MQ0=1;QD=49.23;SB=-1.854e+03	GT:AD:DP:GQ:PL	1/1:24,138:158:99:7976,476,0
chrM	43084	.	A	AT	5953	PASS	AC=2;AF=1.00;AN=2;DP=203;DS;FS=0.000;HaplotypeScore=45.6744;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=29.33;RPA=8,9;RU=T;SB=-2.317e+03;STR	GT:AD:DP:GQ:PL	1/1:12,191:203:99:5953,595,0
chrM	44795	.	A	AT	4542	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.709;DP=160;DS;FS=3.401;HaplotypeScore=100.1822;MLEAC=2;MLEAF=1.00;MQ=58.30;MQ0=0;MQRankSum=1.594;QD=28.39;RPA=8,9;RU=T;ReadPosRankSum=-1.113;SB=-1.913e+03;STR	GT:AD:DP:GQ:PL	1/1:15,144:160:99:4542,433,0
chrM	63582	.	TTAAGTA	T	3810	PASS	AC=2;AF=1.00;AN=2;DP=214;DS;FS=0.000;HaplotypeScore=61.6474;MLEAC=2;MLEAF=1.00;MQ=61.22;MQ0=1;QD=17.80;RPA=11,10;RU=TAAGTA;SB=-4.270e+02;STR	GT:AD:DP:GQ:PL	1/1:147,66:213:99:3810,202,0
chrM	73114	.	AG	A	2754.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.540;DP=96;FS=0.000;HaplotypeScore=232.6029;MLEAC=2;MLEAF=1.00;MQ=58.73;MQ0=0;MQRankSum=1.655;QD=28.70;RPA=6,5;RU=G;ReadPosRankSum=1.001;SB=-6.260e+02;STR	GT:AD:DP:GQ:PL	1/1:12,83:96:99:2797,264,0
chrM	73136	.	TC	T	2031.96	PASS	AC=2;AF=1.00;AN=2;DP=62;FS=0.000;HaplotypeScore=255.1568;MLEAC=2;MLEAF=1.00;MQ=57.64;MQ0=0;QD=32.77;RPA=3,2;RU=C;SB=-5.010e+02;STR	GT:AD:DP:GQ:PL	1/1:14,46:62:99:2074,178,0
chrV	117045	.	A	AAGCT	399.10	filter	AC=2;AF=1.00;AN=2;DP=6;FS=0.000;HaplotypeScore=10.3309;MLEAC=2;MLEAF=1.00;MQ=45.23;MQ0=0;QD=66.52;SB=-8.144e-04	GT:AD:DP:GQ:PL	1/1:1,5:6:18:441,18,0
chrV	261464	.	C	CA	908.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-3.301;DP=122;FS=2.521;HaplotypeScore=104.3661;MLEAC=2;MLEAF=1.00;MQ=63.37;MQ0=0;MQRankSum=2.966;QD=7.45;RPA=22,23;RU=A;ReadPosRankSum=-1.026;SB=-1.390e+02;STR	GT:AD:DP:GQ:PL	1/1:76,42:122:95:951,95,0
chrV	272558	.	GT	G	2827.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.471;DP=138;FS=0.000;HaplotypeScore=48.4341;MLEAC=2;MLEAF=1.00;MQ=60.22;MQ0=0;MQRankSum=0.386;QD=20.49;RPA=12,11;RU=T;ReadPosRankSum=0.358;SB=-1.216e+03;STR	GT:AD:DP:GQ:PL	1/1:30,97:138:39:2870,39,0
chrVI	11068	.	CT	C	2305.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=0.111;DP=246;FS=1.353;HaplotypeScore=124.0635;MLEAC=1;MLEAF=0.500;MQ=41.25;MQ0=4;MQRankSum=-2.059;QD=9.37;RPA=14,13;RU=T;ReadPosRankSum=0.295;SB=-6.190e+02;STR	GT:AD:DP:GQ:PL	0/1:146,92:240:99:2345,0,2546
chrVI	97864	.	C	CTT	5661	PASS	AC=2;AF=1.00;AN=2;DP=151;FS=0.000;HaplotypeScore=121.4536;MLEAC=2;MLEAF=1.00;MQ=59.09;MQ0=0;QD=37.49;RPA=10,12;RU=T;SB=-1.487e+03;STR	GT:AD:DP:GQ:PL	1/1:13,124:151:99:5661,403,0
chrVI	106277	.	C	CTT	4434	PASS	AC=2;AF=1.00;AN=2;DP=161;FS=0.000;HaplotypeScore=139.4092;MLEAC=2;MLEAF=1.00;MQ=66.22;MQ0=0;QD=27.54;RPA=13,15;RU=T;SB=-5.160e+02;STR	GT:AD:DP:GQ:PL	1/1:27,131:161:99:4434,397,0
chrVII	214	.	A	AC	1794.96	PASS	AC=2;AF=1.00;AN=2;DP=50;FS=0.000;HaplotypeScore=7.1629;MLEAC=2;MLEAF=1.00;MQ=36.31;MQ0=0;QD=35.90;RPA=2,3;RU=C;SB=-6.340e+02;STR	GT:AD:DP:GQ:PL	1/1:2,46:48:99:1837,132,0
chrVII	8151	.	G	GA	660.96	filter	AC=2;AF=1.00;AN=2;DP=38;FS=0.000;HaplotypeScore=1.4160;MLEAC=2;MLEAF=1.00;MQ=38.69;MQ0=19;QD=17.39;RPA=1,2;RU=A;SB=-3.050e+02;STR	GT:AD:DP:GQ:PL	1/1:2,35:17:48:703,48,0
chrVII	397834	.	GA	G	1668.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.593;DP=174;FS=15.028;HaplotypeScore=248.7003;MLEAC=1;MLEAF=0.500;MQ=64.15;MQ0=0;MQRankSum=5.638;QD=9.59;RPA=20,19;RU=A;ReadPosRankSum=-1.407;SB=-8.048e+01;STR	GT:AD:DP:GQ:PL	0/1:68,100:174:99:1708,0,115
chrVII	405085	.	CG	C	5351	PASS	AC=2;AF=1.00;AN=2;DP=139;FS=0.000;HaplotypeScore=25.8522;MLEAC=2;MLEAF=1.00;MQ=49.90;MQ0=2;QD=38.50;RPA=2,1;RU=G;SB=-8.600e+02;STR	GT:AD:DP:GQ:PL	1/1:0,139:124:99:5351,373,0
chrVII	496729	.	T	TA	2116.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.928;DP=94;FS=18.419;HaplotypeScore=64.7728;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;MQRankSum=-0.011;QD=22.52;RPA=13,14;RU=A;ReadPosRankSum=1.976;SB=-8.590e+02;STR	GT:AD:DP:GQ:PL	1/1:24,70:94:66:2159,66,0
chrVII	733109	.	AT	A	537.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.894;DP=145;FS=2.811;HaplotypeScore=128.0066;MLEAC=1;MLEAF=0.500;MQ=60.66;MQ0=0;MQRankSum=0.387;QD=3.71;RPA=20,19;RU=T;ReadPosRankSum=-0.455;SB=-2.430e+02;STR	GT:AD:DP:GQ:PL	0/1:99,29:145:99:577,0,1598
chrVIII	2292	.	G	GC	1111.01	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.037;DP=70;FS=2.090;HaplotypeScore=45.6098;MLEAC=1;MLEAF=0.500;MQ=46.98;MQ0=0;MQRankSum=1.220;QD=15.87;RPA=11,12;RU=C;ReadPosRankSum=-0.666;SB=-5.060e+02;STR	GT:AD:DP:GQ:PL	0/1:25,43:69:17:1150,0,17
chrVIII	17534	.	A	AT	2835.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.734;DP=122;FS=4.023;HaplotypeScore=85.6065;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=0.958;QD=23.25;RPA=11,12;RU=T;ReadPosRankSum=-0.584;SB=-1.380e+03;STR	GT:AD:DP:GQ:PL	0/1:25,91:122:41:2875,0,41
chrVIII	85508	.	TTA	T	6099	PASS	AC=2;AF=1.00;AN=2;DP=164;FS=0.000;HaplotypeScore=40.5018;MLEAC=2;MLEAF=1.00;MQ=50.24;MQ0=0;QD=37.19;RPA=4,3;RU=TA;SB=-2.331e+03;STR	GT:AD:DP:GQ:PL	1/1:26,138:160:99:6099,415,0
chrVIII	396945	.	GA	G	280.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.088;DP=98;FS=0.000;HaplotypeScore=144.8729;MLEAC=1;MLEAF=0.500;MQ=60.14;MQ0=0;MQRankSum=-0.780;QD=2.87;RPA=19,18;RU=A;ReadPosRankSum=0.594;SB=-1.580e+02;STR	GT:AD:DP:GQ:PL	0/1:69,16:98:99:320,0,1241
chrVIII	475931	.	TTA	T	2012.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.517;DP=125;FS=0.000;HaplotypeScore=60.2834;MLEAC=2;MLEAF=1.00;MQ=60.47;MQ0=0;MQRankSum=0.881;QD=16.10;RPA=11,10;RU=TA;ReadPosRankSum=-0.395;SB=-6.870e+02;STR	GT:AD:DP:GQ:PL	1/1:68,51:125:99:2055,128,0
chrVIII	549799	.	TCA	T	568.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=4.709;DP=72;FS=138.104;HaplotypeScore=170.3102;MLEAC=1;MLEAF=0.500;MQ=34.20;MQ0=15;MQRankSum=1.938;QD=7.90;ReadPosRankSum=-5.325;SB=-3.011e+00	GT:AD:DP:GQ:PL	0/1:49,21:56:99:608,0,1641
chrVIII	562385	.	AT	A	1088.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.096;DP=250;DS;FS=6.351;HaplotypeScore=522.7874;MLEAC=1;MLEAF=0.500;MQ=24.77;MQ0=106;MQRankSum=0.895;QD=4.36;RPA=12,11;RU=T;ReadPosRankSum=0.272;SB=-2.520e+02;STR	GT:AD:DP:GQ:PL	0/1:173,70:135:99:1128,0,2020
chrX	470130	.	GTAA	G	2726.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.293;DP=97;FS=2.627;HaplotypeScore=47.8780;MLEAC=2;MLEAF=1.00;MQ=60.79;MQ0=0;MQRankSum=0.185;QD=28.11;RPA=16,15;RU=TAA;ReadPosRankSum=-0.985;SB=-1.001e+03;STR	GT:AD:DP:GQ:PL	1/1:30,59:97:65:2769,65,0
chrX	640784	.	G	GA	5141	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.367;DP=154;FS=2.536;HaplotypeScore=51.5399;MLEAC=2;MLEAF=1.00;MQ=59.68;MQ0=0;MQRankSum=-0.193;QD=33.38;RPA=10,11;RU=A;ReadPosRankSum=1.353;SB=-1.508e+03;STR	GT:AD:DP:GQ:PL	1/1:8,144:154:99:5141,356,0
chrXI	457	.	C	CA	3651	PASS	AC=2;AF=1.00;AN=2;DP=79;FS=0.000;HaplotypeScore=22.5870;MLEAC=2;MLEAF=1.00;MQ=58.72;MQ0=0;QD=46.22;SB=-1.545e+03	GT:AD:DP:GQ:PL	1/1:1,78:79:99:3651,235,0
chrXI	68454	.	G	GCC	6557	PASS	AC=2;AF=1.00;AN=2;DP=117;FS=0.000;HaplotypeScore=424.3884;MLEAC=2;MLEAF=1.00;MQ=55.93;MQ0=0;QD=56.04;SB=-3.248e+03	GT:AD:DP:GQ:PL	1/1:13,104:117:99:6557,352,0
chrXI	68468	.	T	TG	5345	PASS	AC=2;AF=1.00;AN=2;DP=113;FS=0.000;HaplotypeScore=503.7737;MLEAC=2;MLEAF=1.00;MQ=56.44;MQ0=0;QD=47.30;SB=-2.607e+03	GT:AD:DP:GQ:PL	1/1:0,112:113:99:5345,340,0
chrXI	451568	.	GGAACAC	G	9107	PASS	AC=2;AF=1.00;AN=2;DP=128;FS=0.000;HaplotypeScore=10.7677;MLEAC=2;MLEAF=1.00;MQ=60.03;MQ0=0;QD=71.15;RPA=2,1;RU=GAACAC;SB=-4.055e+03;STR	GT:AD:DP:GQ:PL	1/1:21,107:128:99:9107,319,0
chrXI	465172	.	G	GTATA	1487.97	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.950;DP=85;FS=0.000;HaplotypeScore=61.6442;MLEAC=2;MLEAF=1.00;MQ=61.29;MQ0=0;MQRankSum=0.615;QD=17.51;RPA=10,12;RU=TA;ReadPosRankSum=0.280;SB=-3.182e+02;STR	GT:AD:DP:GQ:PL	1/1:55,27:85:28:1530,28,0
chrXI	524035	.	AT	A	647.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.033;DP=193;FS=1.355;HaplotypeScore=431.2331;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=1;MQRankSum=2.077;QD=3.36;RPA=23,22;RU=T;ReadPosRankSum=-0.773;SB=-2.950e+02;STR	GT:AD:DP:GQ:PL	0/1:138,42:192:99:687,0,1589
chrXI	666556	.	GT	G	2759.96	PASS	AC=2;AF=1.00;AN=2;DP=63;FS=0.000;HaplotypeScore=16.5112;MLEAC=2;MLEAF=1.00;MQ=57.43;MQ0=0;QD=43.81;SB=-3.790e+02	GT:AD:DP:GQ:PL	1/1:0,61:62:99:2802,181,0
chrXII	552	.	AT	A	1107.96	filter	AC=2;AF=1.00;AN=2;DP=29;FS=0.000;HaplotypeScore=84.6374;MLEAC=2;MLEAF=1.00;MQ=24.11;MQ0=2;QD=38.21;RPA=2,1;RU=T;SB=-8.144e-04;STR	GT:AD:DP:GQ:PL	1/1:1,27:27:81:1150,81,0
chrXII	591	.	T	TGTACAGC	1677.96	filter	AC=2;AF=1.00;AN=2;DP=21;FS=0.000;HaplotypeScore=76.9940;MLEAC=2;MLEAF=1.00;MQ=23.71;MQ0=0;QD=79.90;SB=-8.144e-04	GT:AD:DP:GQ:PL	1/1:8,12:21:60:1720,60,0
chrXII	11195	.	TAC	T	1869.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.712;DP=196;FS=14.892;HaplotypeScore=470.6267;MLEAC=1;MLEAF=0.500;MQ=31.07;MQ0=78;MQRankSum=-1.291;QD=9.54;RPA=2,1;RU=AC;ReadPosRankSum=4.266;SB=-2.450e+02;STR	GT:AD:DP:GQ:PL	0/1:137,49:117:99:1909,0,3105
chrXII	11225	.	CA	C	3065.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.699;DP=145;FS=15.219;HaplotypeScore=550.2318;MLEAC=1;MLEAF=0.500;MQ=39.44;MQ0=1;MQRankSum=3.352;QD=21.14;ReadPosRankSum=4.716;SB=-1.084e+03	GT:AD:DP:GQ:PL	0/1:58,79:137:99:3105,0,1681
chrXII	52618	.	CT	C	1758.97	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=2.354;DP=136;FS=0.000;HaplotypeScore=53.8496;MLEAC=1;MLEAF=0.500;MQ=60.23;MQ0=0;MQRankSum=0.931;QD=12.93;RPA=15,14;RU=T;ReadPosRankSum=0.552;SB=-8.390e+02;STR	GT:AD:DP:GQ:PL	1/1:46,74:136:98:1801,98,0
chrXII	187137	.	AT	A	7851	PASS	AC=2;AF=1.00;AN=2;DP=200;FS=0.000;HaplotypeScore=51.0944;MLEAC=2;MLEAF=1.00;MQ=60.10;MQ0=0;QD=39.26;RPA=3,2;RU=T;SB=-2.029e+03;STR	GT:AD:DP:GQ:PL	1/1:4,196:200:99:7851,590,0
chrXII	699936	.	AG	A	589.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=4.507;DP=185;FS=160.175;HaplotypeScore=480.9230;MLEAC=1;MLEAF=0.500;MQ=60.42;MQ0=0;MQRankSum=4.742;QD=3.19;ReadPosRankSum=-5.461;SB=-8.144e-04	GT:AD:DP:GQ:PL	0/1:131,49:185:99:629,0,3204
chrXII	784382	.	G	GC	7212	PASS	AC=2;AF=1.00;AN=2;DP=181;FS=0.000;HaplotypeScore=38.3959;MLEAC=2;MLEAF=1.00;MQ=58.25;MQ0=0;QD=39.85;RPA=2,3;RU=C;SB=-2.315e+03;STR	GT:AD:DP:GQ:PL	1/1:2,175:180:99:7212,524,0
chrXII	881947	.	C	CAT	2018.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.021;DP=139;FS=1.618;HaplotypeScore=99.5875;MLEAC=1;MLEAF=0.500;MQ=60.32;MQ0=1;MQRankSum=-0.328;QD=14.52;RPA=11,12;RU=AT;ReadPosRankSum=-0.899;SB=-8.250e+02;STR	GT:AD:DP:GQ:PL	0/1:73,52:138:90:2058,0,90
chrXII	1012324	.	C	CG	4343	PASS	AC=2;AF=1.00;AN=2;DP=118;FS=0.000;HaplotypeScore=496.6023;MLEAC=2;MLEAF=1.00;MQ=56.05;MQ0=0;QD=36.81;RPA=1,2;RU=G;SB=-1.235e+03;STR	GT:AD:DP:GQ:PL	1/1:30,86:118:99:4343,331,0
chrXII	1012328	.	A	AGCC	4807	PASS	AC=2;AF=1.00;AN=2;DP=93;FS=0.000;HaplotypeScore=395.8947;MLEAC=2;MLEAF=1.00;MQ=55.42;MQ0=0;QD=51.69;RPA=1,2;RU=GCC;SB=-2.610e+02;STR	GT:AD:DP:GQ:PL	1/1:9,83:93:99:4807,247,0
chrXIII	238763	.	CT	C	964.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.499;DP=198;FS=8.614;HaplotypeScore=692.4975;MLEAC=1;MLEAF=0.500;MQ=55.69;MQ0=1;MQRankSum=-0.063;QD=4.87;RPA=24,23;RU=T;ReadPosRankSum=0.188;SB=-2.300e+02;STR	GT:AD:DP:GQ:PL	0/1:146,23:197:99:1004,0,1654
chrXIII	918120	.	C	CT	830.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.552;DP=89;FS=7.334;HaplotypeScore=69.6400;MLEAC=1;MLEAF=0.500;MQ=57.48;MQ0=1;MQRankSum=1.967;QD=9.34;RPA=19,20;RU=T;ReadPosRankSum=-2.703;SB=-2.910e+02;STR	GT:AD:DP:GQ:PL	0/1:28,48:87:48:870,0,48
chrXIII	921418	.	CT	C	2070.96	filter	AC=2;AF=1.00;AN=2;BaseQRankSum=0.882;DP=106;FS=2.158;HaplotypeScore=115.4357;MLEAC=2;MLEAF=1.00;MQ=40.39;MQ0=14;MQRankSum=1.794;QD=19.54;RPA=14,13;RU=T;ReadPosRankSum=0.638;SB=-7.900e+02;STR	GT:AD:DP:GQ:PL	1/1:25,73:90:99:2113,115,0
chrXIV	6636	.	CA	C	2179.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.780;DP=134;DS;FS=21.877;HaplotypeScore=677.8124;MLEAC=1;MLEAF=0.500;MQ=33.34;MQ0=13;MQRankSum=2.057;QD=16.27;ReadPosRankSum=3.355;SB=-7.760e+02	GT:AD:DP:GQ:PL	0/1:77,52:108:99:2219,0,844
chrXIV	7478	.	A	AT	2312.96	filter	AC=2;AF=1.00;AN=2;DP=98;FS=0.000;HaplotypeScore=7.0475;MLEAC=2;MLEAF=1.00;MQ=22.40;MQ0=14;QD=23.60;SB=-8.144e-04	GT:AD:DP:GQ:PL	1/1:1,97:51:99:2355,154,0
chrXIV	312328	.	AACG	A	8579	PASS	AC=2;AF=1.00;AN=2;DP=163;FS=0.000;HaplotypeScore=25.7358;MLEAC=2;MLEAF=1.00;MQ=60.46;MQ0=0;QD=52.63;RPA=3,2;RU=ACG;SB=-3.510e+03;STR	GT:AD:DP:GQ:PL	1/1:14,149:163:99:8579,446,0
chrXIV	439397	.	G	GT	6329	PASS	AC=2;AF=1.00;AN=2;DP=179;FS=0.000;HaplotypeScore=42.3321;MLEAC=2;MLEAF=1.00;MQ=60.05;MQ0=0;QD=35.36;RPA=6,7;RU=T;SB=-2.931e+03;STR	GT:AD:DP:GQ:PL	1/1:7,171:179:99:6329,518,0
chrXIV	779305	.	AGTC	A	297.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.618;DP=159;FS=401.033;HaplotypeScore=564.0049;MLEAC=1;MLEAF=0.500;MQ=61.81;MQ0=1;MQRankSum=9.159;QD=1.87;ReadPosRankSum=-9.181;SB=-3.011e+00	GT:AD:DP:GQ:PL	0/1:107,51:158:99:337,0,5424
chrXV	90	.	CCCA	C	2933.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.674;DP=66;FS=17.130;HaplotypeScore=135.3252;MLEAC=1;MLEAF=0.500;MQ=49.48;MQ0=1;MQRankSum=3.381;QD=44.45;ReadPosRankSum=2.240;SB=-3.650e+02	GT:AD:DP:GQ:PL	0/1:15,49:59:36:2973,0,36
chrXV	522811	.	G	GAA	1185.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.488;DP=155;FS=4.787;HaplotypeScore=351.1050;MLEAC=1;MLEAF=0.500;MQ=63.56;MQ0=0;MQRankSum=7.309;QD=7.65;RPA=28,30;RU=A;ReadPosRankSum=0.298;SB=-5.360e+02;STR	GT:AD:DP:GQ:PL	0/1:96,59:155:99:1225,0,702
chrXV	722438	.	G	GGT	171.10	filter	AC=2;AF=1.00;AN=2;DP=6;FS=0.000;HaplotypeScore=59.2342;MLEAC=2;MLEAF=1.00;MQ=63.51;MQ0=0;QD=28.52;SB=-8.144e-04	GT:AD:DP:GQ:PL	1/1:0,6:6:18:213,18,0
chrXVI	144689	.	AGGAAACGTC	A	12048	PASS	AC=2;AF=1.00;AN=2;DP=151;FS=0.000;HaplotypeScore=23.4845;MLEAC=2;MLEAF=1.00;MQ=43.02;MQ0=0;QD=79.79;RPA=4,3;RU=GGAAACGTC;SB=-2.261e+03;STR	GT:AD:DP:GQ:PL	1/1:40,111:151:99:12048,337,0
chrXVI	481304	.	AT	A	4366	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.596;DP=164;FS=3.024;HaplotypeScore=91.6691;MLEAC=2;MLEAF=1.00;MQ=59.95;MQ0=0;MQRankSum=-0.007;QD=26.62;RPA=13,12;RU=T;ReadPosRankSum=-0.281;SB=-8.850e+02;STR	GT:AD:DP:GQ:PL	1/1:24,135:164:99:4366,334,0
chrXVI	698526	.	GA	G	353.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.289;DP=138;FS=0.000;HaplotypeScore=196.9845;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=0.072;QD=2.56;RPA=17,16;RU=A;ReadPosRankSum=-0.418;SB=-1.780e+02;STR	GT:AD:DP:GQ:PL	0/1:101,25:138:99:393,0,2644