##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/FY1679/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="Wed Jan 15 03:57:22 PST 2014",Epoch=1389787042152,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/FY1679/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	FY1679
chrI	6736	.	C	CAA	1195.07	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.917;DP=118;FS=0.000;HaplotypeScore=36.6121;MLEAC=1;MLEAF=0.500;MQ=60.27;MQ0=1;MQRankSum=0.713;QD=10.13;RPA=19,21;RU=A;ReadPosRankSum=0.917;SB=-1.891e+02;STR	GT:AD:DP:GQ:PL	1/1:69,41:117:99:1237,102,0
chrI	19971	.	C	CCT	2691.96	filter	AC=2;AF=1.00;AN=2;DP=125;DS;FS=0.000;HaplotypeScore=11.9477;MLEAC=2;MLEAF=1.00;MQ=24.03;MQ0=27;QD=21.54;SB=-1.202e+03	GT:AD:DP:GQ:PL	1/1:0,119:58:99:2734,169,0
chrI	23712	.	C	CA	562.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.196;DP=125;FS=0.000;HaplotypeScore=303.3418;MLEAC=1;MLEAF=0.500;MQ=51.65;MQ0=0;MQRankSum=2.141;QD=4.50;RPA=24,25;RU=A;ReadPosRankSum=1.455;SB=-1.050e+02;STR	GT:AD:DP:GQ:PL	0/1:75,9:125:99:602,0,164
chrI	126880	.	C	CT,CTT	6444	PASS	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-3.017;DP=249;DS;FS=12.913;HaplotypeScore=282.0160;MLEAC=1,1;MLEAF=0.500,0.500;MQ=64.62;MQ0=0;MQRankSum=2.450;QD=25.88;RPA=15,16,17;RU=T;ReadPosRankSum=0.266;SB=-1.768e+03;STR	GT:AD:DP:GQ:PL	1/2:39,10,196:249:76:6444,3433,2931,533,0,76
chrI	183387	.	AC	A	7181	filter	AC=2;AF=1.00;AN=2;DP=201;DS;FS=0.000;HaplotypeScore=31.6936;MLEAC=2;MLEAF=1.00;MQ=37.87;MQ0=6;QD=35.73;RPA=2,1;RU=C;SB=-3.469e+03;STR	GT:AD:DP:GQ:PL	1/1:1,199:180:99:7181,536,0
chrI	206176	.	CG	C	4002	filter	AC=2;AF=1.00;AN=2;DP=107;FS=0.000;HaplotypeScore=631.2289;MLEAC=2;MLEAF=1.00;MQ=29.21;MQ0=6;QD=37.40;SB=-1.817e+03	GT:AD:DP:GQ:PL	1/1:45,62:93:99:4002,280,0
chrI	206179	.	A	AC	3597	filter	AC=2;AF=1.00;AN=2;DP=120;FS=0.000;HaplotypeScore=697.4118;MLEAC=2;MLEAF=1.00;MQ=28.53;MQ0=7;QD=29.98;RPA=1,2;RU=C;SB=-1.558e+03;STR	GT:AD:DP:GQ:PL	1/1:58,62:101:99:3597,303,0
chrII	7912	.	GA	G	1015.96	filter	AC=2;AF=1.00;AN=2;DP=85;FS=0.000;HaplotypeScore=11.7621;MLEAC=2;MLEAF=1.00;MQ=25.10;MQ0=14;QD=11.95;RPA=3,2;RU=A;SB=-3.640e+02;STR	GT:AD:DP:GQ:PL	1/1:26,57:51:78:1058,78,0
chrII	9022	.	G	GA	1010.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.516;DP=171;FS=1.103;HaplotypeScore=120.3325;MLEAC=1;MLEAF=0.500;MQ=56.52;MQ0=0;MQRankSum=2.698;QD=5.91;RPA=20,21;RU=A;ReadPosRankSum=-1.877;SB=-5.090e+02;STR	GT:AD:DP:GQ:PL	0/1:100,47:170:99:1050,0,118
chrII	88484	.	GGAGAA	G	17325	PASS	AC=2;AF=1.00;AN=2;DP=243;DS;FS=0.000;HaplotypeScore=58.0208;MLEAC=2;MLEAF=1.00;MQ=51.05;MQ0=0;QD=71.30;RPA=2,1;RU=GAGAA;SB=-3.891e+03;STR	GT:AD:DP:GQ:PL	1/1:12,230:243:99:17325,692,0
chrII	167978	.	C	CAA,CA	2251.94	PASS	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-2.966;DP=190;DS;FS=2.197;HaplotypeScore=104.1929;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.15;MQ0=0;MQRankSum=1.958;QD=11.85;RPA=16,18,17;RU=A;ReadPosRankSum=-1.907;SB=-4.250e+02;STR	GT:AD:DP:GQ:PL	1/2:92,12,83:188:99:2330,684,885,338,0,360
chrII	221288	.	AGT	A	3622	PASS	AC=2;AF=1.00;AN=2;DP=85;FS=0.000;HaplotypeScore=45.3245;MLEAC=2;MLEAF=1.00;MQ=34.40;MQ0=1;QD=42.61;RPA=2,1;RU=GT;SB=-8.580e+02;STR	GT:AD:DP:GQ:PL	1/1:4,80:81:99:3622,235,0
chrII	263144	.	GC	G	922.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.473;DP=23;FS=3.424;HaplotypeScore=249.8012;MLEAC=2;MLEAF=1.00;MQ=30.92;MQ0=0;MQRankSum=1.103;QD=40.13;ReadPosRankSum=-0.315;SB=-4.130e+02	GT:AD:DP:GQ:PL	1/1:13,9:23:60:965,60,0
chrII	263158	.	CG	C	1399.96	PASS	AC=2;AF=1.00;AN=2;DP=35;FS=0.000;HaplotypeScore=348.5539;MLEAC=2;MLEAF=1.00;MQ=33.81;MQ0=0;QD=40.00;RPA=2,1;RU=G;SB=-3.940e+02;STR	GT:AD:DP:GQ:PL	1/1:0,35:35:99:1442,105,0
chrII	263168	.	CG	C	2194.96	PASS	AC=2;AF=1.00;AN=2;DP=55;FS=0.000;HaplotypeScore=337.2479;MLEAC=2;MLEAF=1.00;MQ=39.60;MQ0=0;QD=39.91;SB=-6.510e+02	GT:AD:DP:GQ:PL	1/1:2,50:54:99:2237,153,0
chrII	383176	.	C	CG	7594	PASS	AC=2;AF=1.00;AN=2;DP=212;FS=0.000;HaplotypeScore=46.5892;MLEAC=2;MLEAF=1.00;MQ=60.53;MQ0=0;QD=35.82;RPA=2,3;RU=G;SB=-2.886e+03;STR	GT:AD:DP:GQ:PL	1/1:1,203:212:99:7594,608,0
chrII	389425	.	T	TTG	8113	PASS	AC=2;AF=1.00;AN=2;DP=169;FS=0.000;HaplotypeScore=1102.4917;MLEAC=2;MLEAF=1.00;MQ=48.66;MQ0=0;QD=48.01;SB=-3.612e+03	GT:AD:DP:GQ:PL	1/1:17,20:169:99:8113,493,0
chrII	389429	.	CG	C	5527	PASS	AC=2;AF=1.00;AN=2;DP=149;FS=0.000;HaplotypeScore=1183.2025;MLEAC=2;MLEAF=1.00;MQ=47.65;MQ0=0;QD=37.09;SB=-2.626e+03	GT:AD:DP:GQ:PL	1/1:23,126:149:99:5527,448,0
chrII	723663	.	C	CA	2749.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.982;DP=206;FS=1.125;HaplotypeScore=154.1574;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=2.732;QD=13.35;RPA=15,16;RU=A;ReadPosRankSum=-1.140;SB=-9.280e+02;STR	GT:AD:DP:GQ:PL	0/1:81,114:206:99:2789,0,106
chrII	746362	.	CATCTGCA	C	20557	PASS	AC=2;AF=1.00;AN=2;DP=243;FS=0.000;HaplotypeScore=24.4976;MLEAC=2;MLEAF=1.00;MQ=60.59;MQ0=0;QD=84.60;RPA=2,1;RU=ATCTGCA;SB=-7.984e+03;STR	GT:AD:DP:GQ:PL	1/1:22,221:242:99:20557,662,0
chrII	809794	.	AT	A	961.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=1.682;DP=156;FS=11.953;HaplotypeScore=114.4240;MLEAC=1;MLEAF=0.500;MQ=45.75;MQ0=13;MQRankSum=-1.016;QD=6.17;RPA=19,18;RU=T;ReadPosRankSum=0.100;SB=-4.200e+02;STR	GT:AD:DP:GQ:PL	0/1:88,51:131:69:1001,0,69
chrIII	162712	.	TA	T	4677	PASS	AC=2;AF=1.00;AN=2;DP=165;FS=0.000;HaplotypeScore=645.9474;MLEAC=2;MLEAF=1.00;MQ=59.53;MQ0=0;QD=28.35;RPA=10,9;RU=A;SB=-2.177e+03;STR	GT:AD:DP:GQ:PL	1/1:15,150:165:99:4677,451,0
chrIII	163163	.	G	GA	5621	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.988;DP=192;FS=3.035;HaplotypeScore=542.2563;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=0;MQRankSum=1.302;QD=29.28;RPA=9,10;RU=A;ReadPosRankSum=1.341;SB=-2.703e+03;STR	GT:AD:DP:GQ:PL	1/1:16,166:192:99:5621,499,0
chrIII	163192	.	A	AT	6455	PASS	AC=2;AF=1.00;AN=2;DP=182;FS=0.000;HaplotypeScore=503.3715;MLEAC=2;MLEAF=1.00;MQ=60.18;MQ0=0;QD=35.47;RPA=3,4;RU=T;SB=-2.517e+03;STR	GT:AD:DP:GQ:PL	1/1:6,176:182:99:6455,533,0
chrIV	126537	.	C	CTT	1129.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.538;DP=215;DS;FS=14.744;HaplotypeScore=555.1702;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=0;MQRankSum=4.775;QD=5.26;RPA=28,30;RU=T;ReadPosRankSum=1.370;SB=-3.900e+02;STR	GT:AD:DP:GQ:PL	0/1:160,51:214:99:1169,0,618
chrIV	169891	.	TA	T	903.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.716;DP=245;DS;FS=10.273;HaplotypeScore=892.4890;MLEAC=1;MLEAF=0.500;MQ=55.64;MQ0=0;MQRankSum=0.810;QD=3.69;RPA=18,17;RU=A;ReadPosRankSum=0.512;SB=-8.400e+01;STR	GT:AD:DP:GQ:PL	0/1:166,46:244:99:943,0,3449
chrIV	344004	.	G	GTA	2993.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.537;DP=243;DS;FS=1.861;HaplotypeScore=141.7400;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.499;QD=12.32;RPA=13,14;RU=TA;ReadPosRankSum=-0.114;SB=-1.310e+03;STR	GT:AD:DP:GQ:PL	0/1:145,85:243:99:3033,0,775
chrIV	403511	.	G	GT	6407	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=1.039;DP=210;FS=2.635;HaplotypeScore=122.5303;MLEAC=2;MLEAF=1.00;MQ=59.81;MQ0=0;MQRankSum=-0.082;QD=30.51;RPA=9,10;RU=T;ReadPosRankSum=-0.372;SB=-1.974e+03;STR	GT:AD:DP:GQ:PL	1/1:11,188:209:99:6407,520,0
chrIV	688062	.	C	CTTT,CTT	7148	PASS	AC=1,1;AF=0.500,0.500;AN=2;DP=242;FS=0.000;HaplotypeScore=128.1847;MLEAC=1,1;MLEAF=0.500,0.500;MQ=57.71;MQ0=0;QD=29.54;RPA=14,17,16;RU=T;SB=-2.887e+03;STR	GT:AD:DP:GQ:PL	1/2:158,9,60:240:99:7148,2169,1690,769,0,181
chrIV	817531	.	T	TA	6404	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=1.046;DP=241;FS=7.332;HaplotypeScore=82.5679;MLEAC=2;MLEAF=1.00;MQ=59.60;MQ0=0;MQRankSum=-0.772;QD=26.57;RPA=10,11;RU=A;ReadPosRankSum=0.812;SB=-2.539e+03;STR	GT:AD:DP:GQ:PL	1/1:38,199:241:99:6404,339,0
chrIV	1150910	.	A	AG	7342	PASS	AC=2;AF=1.00;AN=2;DP=209;DS;FS=0.000;HaplotypeScore=38.7621;MLEAC=2;MLEAF=1.00;MQ=56.41;MQ0=0;QD=35.13;RPA=2,3;RU=G;SB=-3.449e+03;STR	GT:AD:DP:GQ:PL	1/1:7,200:200:99:7342,578,0
chrIV	1305680	.	TG	T	6905	PASS	AC=2;AF=1.00;AN=2;DP=180;FS=0.000;HaplotypeScore=42.3522;MLEAC=2;MLEAF=1.00;MQ=59.00;MQ0=0;QD=38.36;RPA=2,1;RU=G;SB=-2.300e+03;STR	GT:AD:DP:GQ:PL	1/1:1,167:180:99:6905,503,0
chrIV	1515034	.	TA	T	7632	PASS	AC=2;AF=1.00;AN=2;DP=250;DS;FS=0.000;HaplotypeScore=93.9414;MLEAC=2;MLEAF=1.00;MQ=58.79;MQ0=0;QD=30.53;RPA=11,10;RU=A;SB=-2.527e+03;STR	GT:AD:DP:GQ:PL	1/1:10,237:249:99:7632,723,0
chrIV	1518948	.	G	GT	4447	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.149;DP=189;DS;FS=2.696;HaplotypeScore=105.5949;MLEAC=1;MLEAF=0.500;MQ=60.07;MQ0=1;MQRankSum=1.653;QD=23.53;RPA=13,14;RU=T;ReadPosRankSum=-0.991;SB=-8.911e+02;STR	GT:AD:DP:GQ:PL	0/1:31,147:188:14:4447,0,14
chrIV	1525376	.	TG	T	4724	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=8.100;DP=246;DS;FS=125.315;HaplotypeScore=7374.1784;MLEAC=1;MLEAF=0.500;MQ=28.78;MQ0=2;MQRankSum=-0.451;QD=19.20;RPA=3,2;RU=G;ReadPosRankSum=6.494;SB=-2.240e+02;STR	GT:AD:DP:GQ:PL	0/1:124,113:234:99:4724,0,452
chrIV	1525391	.	GT	G	2557.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=9.945;DP=246;DS;FS=133.637;HaplotypeScore=5286.4560;MLEAC=1;MLEAF=0.500;MQ=29.22;MQ0=14;MQRankSum=-1.678;QD=10.40;ReadPosRankSum=5.122;SB=-8.144e-04	GT:AD:DP:GQ:PL	0/1:173,64:218:99:2597,0,2386
chrIX	39373	.	T	TA	4879	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.208;DP=184;DS;FS=0.000;HaplotypeScore=68.4603;MLEAC=2;MLEAF=1.00;MQ=59.23;MQ0=0;MQRankSum=-1.533;QD=26.52;RPA=11,12;RU=A;ReadPosRankSum=0.404;SB=-1.285e+03;STR	GT:AD:DP:GQ:PL	1/1:18,154:184:99:4879,340,0
chrIX	57277	.	C	CA	1858.98	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.565;DP=166;FS=11.864;HaplotypeScore=164.3222;MLEAC=1;MLEAF=0.500;MQ=62.34;MQ0=0;MQRankSum=3.190;QD=11.20;RPA=16,17;RU=A;ReadPosRankSum=-2.681;SB=-9.390e+02;STR	GT:AD:DP:GQ:PL	0/1:64,96:166:26:1898,0,26
chrIX	105433	.	A	AAAT	7180	PASS	AC=2;AF=1.00;AN=2;DP=146;FS=0.000;HaplotypeScore=65.4461;MLEAC=2;MLEAF=1.00;MQ=60.48;MQ0=0;QD=49.18;RPA=3,4;RU=AAT;SB=-3.224e+03;STR	GT:AD:DP:GQ:PL	1/1:11,135:146:99:7180,406,0
chrIX	245961	.	TC	T	773.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=6.027;DP=159;FS=312.830;HaplotypeScore=86.1435;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=1;MQRankSum=6.538;QD=4.87;ReadPosRankSum=-8.603;SB=-2.371e+00	GT:AD:DP:GQ:PL	0/1:109,49:157:99:813,0,3009
chrIX	254003	.	TA	T	3839	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.074;DP=227;DS;FS=0.000;HaplotypeScore=96.0867;MLEAC=2;MLEAF=1.00;MQ=59.15;MQ0=1;MQRankSum=1.554;QD=16.91;RPA=15,14;RU=A;ReadPosRankSum=0.035;SB=-1.432e+03;STR	GT:AD:DP:GQ:PL	1/1:74,134:224:99:3839,252,0
chrM	20345	.	GA	G	7139	PASS	AC=2;AF=1.00;AN=2;DP=249;DS;FS=0.000;HaplotypeScore=82.3631;MLEAC=2;MLEAF=1.00;MQ=59.01;MQ0=0;QD=28.67;RPA=3,2;RU=A;SB=-2.627e+03;STR	GT:AD:DP:GQ:PL	1/1:15,233:249:99:7139,742,0
chrM	33618	.	T	TTC	9326	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-2.975;DP=202;DS;FS=11.184;HaplotypeScore=234.5746;MLEAC=2;MLEAF=1.00;MQ=57.68;MQ0=1;MQRankSum=2.924;QD=46.17;ReadPosRankSum=2.591;SB=-2.435e+03	GT:AD:DP:GQ:PL	1/1:30,171:201:99:9326,581,0
chrM	43084	.	A	AT	6336	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.732;DP=249;DS;FS=0.000;HaplotypeScore=123.5651;MLEAC=2;MLEAF=1.00;MQ=58.97;MQ0=0;MQRankSum=1.689;QD=25.45;RPA=8,9;RU=T;ReadPosRankSum=0.344;SB=-2.209e+03;STR	GT:AD:DP:GQ:PL	1/1:30,218:249:99:6336,721,0
chrM	44795	.	A	AT	4923	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-3.770;DP=205;DS;FS=11.026;HaplotypeScore=308.0307;MLEAC=2;MLEAF=1.00;MQ=57.72;MQ0=0;MQRankSum=3.770;QD=24.01;RPA=8,9;RU=T;ReadPosRankSum=-1.927;SB=-1.682e+03;STR	GT:AD:DP:GQ:PL	1/1:17,186:205:99:4923,514,0
chrM	73114	.	AG	A	5208	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-2.899;DP=200;DS;FS=0.000;HaplotypeScore=543.8835;MLEAC=2;MLEAF=1.00;MQ=57.01;MQ0=0;MQRankSum=2.888;QD=26.04;RPA=6,5;RU=G;ReadPosRankSum=0.428;SB=-1.293e+03;STR	GT:AD:DP:GQ:PL	1/1:16,180:199:99:5208,522,0
chrM	73136	.	TC	T	5904	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.507;DP=190;DS;FS=0.000;HaplotypeScore=886.1869;MLEAC=2;MLEAF=1.00;MQ=55.24;MQ0=0;MQRankSum=1.695;QD=31.07;RPA=3,2;RU=C;ReadPosRankSum=0.758;SB=-1.872e+03;STR	GT:AD:DP:GQ:PL	1/1:29,160:190:99:5904,531,0
chrV	261464	.	C	CAA	1410.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-3.605;DP=182;FS=3.317;HaplotypeScore=91.4563;MLEAC=2;MLEAF=1.00;MQ=61.06;MQ0=0;MQRankSum=2.476;QD=7.75;RPA=22,24;RU=A;ReadPosRankSum=-3.720;SB=-1.210e+02;STR	GT:AD:DP:GQ:PL	1/1:113,61:182:76:1453,76,0
chrV	272558	.	GT	G	5755	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.505;DP=234;DS;FS=0.000;HaplotypeScore=96.4193;MLEAC=2;MLEAF=1.00;MQ=59.62;MQ0=2;MQRankSum=0.954;QD=24.59;RPA=12,11;RU=T;ReadPosRankSum=-0.913;SB=-2.671e+03;STR	GT:AD:DP:GQ:PL	1/1:42,184:232:99:5755,489,0
chrVI	11068	.	CT	C	1896.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=0.729;DP=250;DS;FS=15.214;HaplotypeScore=112.9278;MLEAC=1;MLEAF=0.500;MQ=45.18;MQ0=4;MQRankSum=-3.322;QD=7.59;RPA=14,13;RU=T;ReadPosRankSum=1.069;SB=-9.470e+02;STR	GT:AD:DP:GQ:PL	0/1:170,74:244:99:1936,0,2604
chrVI	97864	.	C	CTT	7613	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.464;DP=224;FS=10.231;HaplotypeScore=177.1478;MLEAC=2;MLEAF=1.00;MQ=59.23;MQ0=0;MQRankSum=-0.251;QD=33.99;RPA=10,12;RU=T;ReadPosRankSum=-0.532;SB=-2.300e+03;STR	GT:AD:DP:GQ:PL	1/1:24,181:224:99:7613,443,0
chrVI	106277	.	C	CTT	5590	PASS	AC=2;AF=1.00;AN=2;DP=214;DS;FS=0.000;HaplotypeScore=159.6654;MLEAC=2;MLEAF=1.00;MQ=64.04;MQ0=1;QD=26.12;RPA=13,15;RU=T;SB=-9.750e+02;STR	GT:AD:DP:GQ:PL	1/1:44,169:212:99:5590,514,0
chrVII	214	.	A	AC	4789	PASS	AC=2;AF=1.00;AN=2;DP=150;FS=0.000;HaplotypeScore=17.1177;MLEAC=2;MLEAF=1.00;MQ=36.62;MQ0=1;QD=31.93;RPA=2,3;RU=C;SB=-2.253e+03;STR	GT:AD:DP:GQ:PL	1/1:11,134:141:99:4789,382,0
chrVII	8151	.	G	GA	966.96	filter	AC=2;AF=1.00;AN=2;DP=64;FS=0.000;HaplotypeScore=11.0457;MLEAC=2;MLEAF=1.00;MQ=37.57;MQ0=31;QD=15.11;RPA=1,2;RU=A;SB=-3.810e+02;STR	GT:AD:DP:GQ:PL	1/1:2,61:27:78:1009,78,0
chrVII	397834	.	GAA	G,GA	2576.94	PASS	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-1.675;DP=231;FS=26.710;HaplotypeScore=281.2726;MLEAC=1,1;MLEAF=0.500,0.500;MQ=63.91;MQ0=0;MQRankSum=5.649;QD=11.16;RPA=20,18,19;RU=A;ReadPosRankSum=0.198;SB=-7.300e+01;STR	GT:AD:DP:GQ:PL	1/2:91,9,0:231:99:2655,1243,2460,476,0,528
chrVII	405085	.	CG	C	7623	filter	AC=2;AF=1.00;AN=2;DP=203;FS=0.000;HaplotypeScore=43.7182;MLEAC=2;MLEAF=1.00;MQ=51.53;MQ0=5;QD=37.55;RPA=2,1;RU=G;SB=-9.780e+02;STR	GT:AD:DP:GQ:PL	1/1:2,198:185:99:7623,545,0
chrVII	496729	.	T	TA	2934.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.927;DP=137;FS=0.000;HaplotypeScore=111.0286;MLEAC=2;MLEAF=1.00;MQ=58.76;MQ0=0;MQRankSum=0.661;QD=21.42;RPA=13,14;RU=A;ReadPosRankSum=-0.994;SB=-1.322e+03;STR	GT:AD:DP:GQ:PL	1/1:29,104:137:68:2977,68,0
chrVII	657205	.	A	AC	298.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=8.375;DP=155;FS=289.804;HaplotypeScore=90.7295;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=3.747;QD=1.93;RPA=2,3;RU=C;ReadPosRankSum=-8.714;SB=-2.968e+00;STR	GT:AD:DP:GQ:PL	0/1:101,53:155:99:338,0,3160
chrVII	733109	.	AT	A	651.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.643;DP=250;DS;FS=7.475;HaplotypeScore=210.3597;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=0.332;QD=2.61;RPA=20,19;RU=T;ReadPosRankSum=0.533;SB=-1.790e+02;STR	GT:AD:DP:GQ:PL	0/1:185,27:250:99:691,0,3443
chrVII	1006276	.	G	GC	8537	PASS	AC=2;AF=1.00;AN=2;DP=248;DS;FS=0.000;HaplotypeScore=989.6929;MLEAC=2;MLEAF=1.00;MQ=59.76;MQ0=0;QD=34.42;SB=-3.729e+03	GT:AD:DP:GQ:PL	1/1:184,63:248:99:8537,733,0
chrVII	1006278	.	CG	C	7608	PASS	AC=2;AF=1.00;AN=2;DP=215;DS;FS=0.000;HaplotypeScore=988.5090;MLEAC=2;MLEAF=1.00;MQ=59.83;MQ0=0;QD=35.39;SB=-3.009e+03	GT:AD:DP:GQ:PL	1/1:151,64:215:99:7608,613,0
chrVIII	2292	.	G	GC	1777.01	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.772;DP=139;FS=1.599;HaplotypeScore=109.1705;MLEAC=2;MLEAF=1.00;MQ=45.58;MQ0=0;MQRankSum=0.714;QD=12.78;RPA=11,12;RU=C;ReadPosRankSum=-1.532;SB=-7.530e+02;STR	GT:AD:DP:GQ:PL	1/1:52,82:138:22:1819,22,0
chrVIII	17534	.	A	AT	4536	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.466;DP=178;FS=5.217;HaplotypeScore=96.9828;MLEAC=2;MLEAF=1.00;MQ=60.46;MQ0=0;MQRankSum=0.578;QD=25.48;RPA=11,12;RU=T;ReadPosRankSum=-0.302;SB=-1.988e+03;STR	GT:AD:DP:GQ:PL	1/1:28,147:178:99:4536,229,0
chrVIII	85508	.	TTA	T	9554	PASS	AC=2;AF=1.00;AN=2;DP=250;DS;FS=0.000;HaplotypeScore=54.3665;MLEAC=2;MLEAF=1.00;MQ=50.16;MQ0=1;QD=38.22;RPA=4,3;RU=TA;SB=-4.336e+03;STR	GT:AD:DP:GQ:PL	1/1:30,220:245:99:9554,659,0
chrVIII	396945	.	GA	G	678.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.801;DP=126;FS=13.311;HaplotypeScore=180.3942;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=0;MQRankSum=-1.367;QD=5.39;RPA=19,18;RU=A;ReadPosRankSum=-1.571;SB=-3.590e+02;STR	GT:AD:DP:GQ:PL	0/1:77,31:126:99:718,0,1341
chrVIII	475931	.	TTATA	T,TTA	3221.92	PASS	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.225;DP=172;FS=0.000;HaplotypeScore=91.4492;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.27;MQ0=0;MQRankSum=1.152;QD=18.73;RPA=11,9,10;RU=TA;ReadPosRankSum=-1.443;SB=-1.176e+03;STR	GT:AD:DP:GQ:PL	1/2:76,6,0:172:89:3300,2783,3032,285,0,89
chrVIII	549799	.	TCA	T	783.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=3.615;DP=132;FS=264.843;HaplotypeScore=228.7629;MLEAC=1;MLEAF=0.500;MQ=36.76;MQ0=15;MQRankSum=0.625;QD=5.94;ReadPosRankSum=-6.866;SB=-3.011e+00	GT:AD:DP:GQ:PL	0/1:95,33:106:99:823,0,3193
chrVIII	562385	.	AT	A	745.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=0.961;DP=250;DS;FS=13.882;HaplotypeScore=562.0328;MLEAC=1;MLEAF=0.500;MQ=27.93;MQ0=71;MQRankSum=1.788;QD=2.98;RPA=12,11;RU=T;ReadPosRankSum=-1.189;SB=-1.160e+02;STR	GT:AD:DP:GQ:PL	0/1:188,57:167:99:785,0,2990
chrX	470130	.	GTAA	G	5353	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.703;DP=182;FS=4.393;HaplotypeScore=55.5105;MLEAC=1;MLEAF=0.500;MQ=60.89;MQ0=0;MQRankSum=-0.415;QD=29.41;RPA=16,15;RU=TAA;ReadPosRankSum=0.644;SB=-2.036e+03;STR	GT:AD:DP:GQ:PL	1/1:54,109:182:99:5352,308,0
chrX	639198	.	C	CTTTTTTT	3414	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.582;DP=167;FS=67.454;HaplotypeScore=230.1254;MLEAC=1;MLEAF=0.500;MQ=62.30;MQ0=1;MQRankSum=3.471;QD=20.44;RPA=21,28;RU=T;ReadPosRankSum=1.793;SB=-1.550e+02;STR	GT:AD:DP:GQ:PL	0/1:68,91:166:99:3414,0,153
chrX	640784	.	G	GA	6503	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-2.804;DP=228;DS;FS=2.928;HaplotypeScore=80.9969;MLEAC=2;MLEAF=1.00;MQ=59.62;MQ0=0;MQRankSum=0.700;QD=28.52;RPA=10,11;RU=A;ReadPosRankSum=2.717;SB=-2.280e+03;STR	GT:AD:DP:GQ:PL	1/1:20,202:228:99:6503,357,0
chrXI	457	.	C	CA	10260	PASS	AC=2;AF=1.00;AN=2;DP=243;DS;FS=0.000;HaplotypeScore=50.8656;MLEAC=2;MLEAF=1.00;MQ=57.42;MQ0=0;QD=42.22;SB=-5.096e+03	GT:AD:DP:GQ:PL	1/1:19,222:240:99:10260,719,0
chrXI	68454	.	G	GCC	11435	PASS	AC=2;AF=1.00;AN=2;DP=217;DS;FS=0.000;HaplotypeScore=792.1435;MLEAC=2;MLEAF=1.00;MQ=55.85;MQ0=0;QD=52.70;SB=-5.538e+03	GT:AD:DP:GQ:PL	1/1:16,200:217:99:11435,653,0
chrXI	68468	.	T	TG	9195	PASS	AC=2;AF=1.00;AN=2;DP=213;FS=0.000;HaplotypeScore=984.3249;MLEAC=2;MLEAF=1.00;MQ=56.06;MQ0=0;QD=43.17;SB=-4.392e+03	GT:AD:DP:GQ:PL	1/1:2,201:213:99:9195,638,0
chrXI	451568	.	GGAACAC	G	15651	PASS	AC=2;AF=1.00;AN=2;DP=206;FS=0.000;HaplotypeScore=71.8752;MLEAC=2;MLEAF=1.00;MQ=60.17;MQ0=0;QD=75.98;RPA=2,1;RU=GAACAC;SB=-6.745e+03;STR	GT:AD:DP:GQ:PL	1/1:17,188:206:99:15651,566,0
chrXI	465172	.	G	GTATA	2397.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-3.218;DP=128;FS=2.834;HaplotypeScore=122.1901;MLEAC=2;MLEAF=1.00;MQ=59.95;MQ0=0;MQRankSum=1.038;QD=18.73;RPA=10,12;RU=TA;ReadPosRankSum=-1.143;SB=-6.630e+02;STR	GT:AD:DP:GQ:PL	1/1:77,46:128:63:2440,63,0
chrXI	666556	.	GT	G	10449	PASS	AC=2;AF=1.00;AN=2;DP=249;DS;FS=0.000;HaplotypeScore=146.2302;MLEAC=2;MLEAF=1.00;MQ=57.51;MQ0=0;QD=41.96;SB=-2.703e+03	GT:AD:DP:GQ:PL	1/1:0,249:246:99:10449,740,0
chrXII	552	.	AT	A	1249.96	filter	AC=2;AF=1.00;AN=2;DP=38;FS=0.000;HaplotypeScore=74.5295;MLEAC=2;MLEAF=1.00;MQ=24.31;MQ0=3;QD=32.89;RPA=2,1;RU=T;SB=-8.144e-04;STR	GT:AD:DP:GQ:PL	1/1:7,31:34:90:1292,90,0
chrXII	591	.	T	TGTACAGC	1994.96	filter	AC=2;AF=1.00;AN=2;DP=26;FS=0.000;HaplotypeScore=86.3274;MLEAC=2;MLEAF=1.00;MQ=23.92;MQ0=0;QD=76.73;SB=-8.144e-04	GT:AD:DP:GQ:PL	1/1:13,12:25:72:2037,72,0
chrXII	11195	.	TAC	T	1807.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=5.521;DP=250;DS;FS=0.630;HaplotypeScore=371.8628;MLEAC=1;MLEAF=0.500;MQ=37.13;MQ0=69;MQRankSum=-5.705;QD=7.23;RPA=2,1;RU=AC;ReadPosRankSum=2.606;SB=-8.790e+02;STR	GT:AD:DP:GQ:PL	0/1:186,56:176:99:1847,0,5026
chrXII	187137	.	AT	A	9691	PASS	AC=2;AF=1.00;AN=2;DP=247;DS;FS=0.000;HaplotypeScore=39.3815;MLEAC=2;MLEAF=1.00;MQ=59.66;MQ0=0;QD=39.23;RPA=3,2;RU=T;SB=-2.190e+03;STR	GT:AD:DP:GQ:PL	1/1:4,243:247:99:9691,731,0
chrXII	784382	.	G	GC	7766	PASS	AC=2;AF=1.00;AN=2;DP=208;DS;FS=0.000;HaplotypeScore=47.7374;MLEAC=2;MLEAF=1.00;MQ=58.32;MQ0=0;QD=37.34;RPA=2,3;RU=C;SB=-3.237e+03;STR	GT:AD:DP:GQ:PL	1/1:2,205:208:99:7766,617,0
chrXII	881947	.	C	CAT	2866.98	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=198;FS=5.699;HaplotypeScore=88.3303;MLEAC=1;MLEAF=0.500;MQ=60.06;MQ0=2;MQRankSum=1.285;QD=14.48;RPA=11,12;RU=AT;ReadPosRankSum=0.899;SB=-9.520e+02;STR	GT:AD:DP:GQ:PL	0/1:100,82:196:25:2906,0,25
chrXII	1012324	.	C	CG	6967	PASS	AC=2;AF=1.00;AN=2;DP=199;DS;FS=0.000;HaplotypeScore=751.7011;MLEAC=2;MLEAF=1.00;MQ=57.45;MQ0=0;QD=35.01;RPA=1,2;RU=G;SB=-2.494e+03;STR	GT:AD:DP:GQ:PL	1/1:57,139:199:99:6967,583,0
chrXII	1012328	.	A	AGCC	7247	PASS	AC=2;AF=1.00;AN=2;DP=147;DS;FS=0.000;HaplotypeScore=582.8226;MLEAC=2;MLEAF=1.00;MQ=57.01;MQ0=0;QD=49.30;RPA=1,2;RU=GCC;SB=-5.050e+02;STR	GT:AD:DP:GQ:PL	1/1:17,130:147:99:7247,394,0
chrXIII	387095	.	AT	A	350.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.411;DP=127;DS;FS=1.116;HaplotypeScore=66.9946;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=0.690;QD=2.76;RPA=19,18;RU=T;ReadPosRankSum=-1.606;SB=-1.080e+02;STR	GT:AD:DP:GQ:PL	0/1:95,21:127:99:390,0,1516
chrXIII	698679	.	TA	T	507.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.969;DP=203;DS;FS=0.000;HaplotypeScore=189.0191;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=0.440;QD=2.50;RPA=17,16;RU=A;ReadPosRankSum=-0.069;SB=-2.060e+02;STR	GT:AD:DP:GQ:PL	0/1:150,39:203:99:547,0,3797
chrXIII	908558	.	T	TCAA	2487.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.302;DP=247;DS;FS=3.439;HaplotypeScore=1351.5051;MLEAC=1;MLEAF=0.500;MQ=50.58;MQ0=1;MQRankSum=1.225;QD=10.07;RPA=1,2;RU=CAA;ReadPosRankSum=-3.787;SB=-1.071e+03;STR	GT:AD:DP:GQ:PL	0/1:186,60:231:99:2527,0,9091
chrXIII	918120	.	C	CT	1113.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.237;DP=107;FS=0.000;HaplotypeScore=83.6217;MLEAC=2;MLEAF=1.00;MQ=56.51;MQ0=1;MQRankSum=2.001;QD=10.41;RPA=19,20;RU=T;ReadPosRankSum=-1.565;SB=-5.410e+02;STR	GT:AD:DP:GQ:PL	1/1:42,54:106:88:1156,88,0
chrXIII	921418	.	CTT	C,CT	2410.94	filter	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.796;DP=124;FS=0.000;HaplotypeScore=127.4470;MLEAC=1,1;MLEAF=0.500,0.500;MQ=41.99;MQ0=5;MQRankSum=-0.295;QD=19.44;RPA=14,12,13;RU=T;ReadPosRankSum=1.067;SB=-1.025e+03;STR	GT:AD:DP:GQ:PL	1/2:49,14,0:117:99:2489,2043,2798,173,0,137
chrXIV	6631	.	CCA	C	1576.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.841;DP=244;DS;FS=9.477;HaplotypeScore=1651.5946;MLEAC=1;MLEAF=0.500;MQ=28.11;MQ0=13;MQRankSum=-1.390;QD=6.46;RPA=3,2;RU=CA;ReadPosRankSum=4.282;SB=-2.260e+02;STR	GT:AD:DP:GQ:PL	0/1:166,49:191:99:1616,0,2028
chrXIV	7478	.	A	AT	3465	filter	AC=2;AF=1.00;AN=2;DP=118;DS;FS=0.000;HaplotypeScore=19.7136;MLEAC=2;MLEAF=1.00;MQ=23.89;MQ0=11;QD=29.36;SB=-2.640e+02	GT:AD:DP:GQ:PL	1/1:2,114:81:99:3465,241,0
chrXIV	12975	.	C	CT	376.24	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=1.197;DP=66;FS=0.000;HaplotypeScore=24.0929;MLEAC=1;MLEAF=0.500;MQ=31.38;MQ0=13;MQRankSum=-2.079;QD=5.70;RPA=11,12;RU=T;ReadPosRankSum=0.315;SB=-1.831e+02;STR	GT:AD:DP:GQ:PL	0/1:35,14:38:9:415,0,9
chrXIV	312328	.	AACG	A	11197	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.732;DP=223;FS=0.000;HaplotypeScore=63.9705;MLEAC=2;MLEAF=1.00;MQ=60.01;MQ0=0;MQRankSum=1.715;QD=50.21;RPA=3,2;RU=ACG;ReadPosRankSum=-1.085;SB=-4.242e+03;STR	GT:AD:DP:GQ:PL	1/1:25,197:223:99:11197,573,0
chrXIV	415054	.	C	CTT	3090.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=2.280;DP=237;FS=6.417;HaplotypeScore=1490.1202;MLEAC=2;MLEAF=1.00;MQ=64.47;MQ0=0;MQRankSum=4.709;QD=13.04;RPA=16,18;RU=T;ReadPosRankSum=-1.420;SB=-1.207e+03;STR	GT:AD:DP:GQ:PL	1/1:60,173:237:99:3133,223,0
chrXIV	439397	.	G	GT	7073	PASS	AC=2;AF=1.00;AN=2;DP=208;DS;FS=0.000;HaplotypeScore=49.5449;MLEAC=2;MLEAF=1.00;MQ=60.49;MQ0=0;QD=34.00;RPA=6,7;RU=T;SB=-3.464e+03;STR	GT:AD:DP:GQ:PL	1/1:5,203:208:99:7073,614,0
chrXIV	779308	.	C	CAAAAA	5688	PASS	AC=2;AF=1.00;AN=2;DP=153;FS=0.000;HaplotypeScore=168.0344;MLEAC=2;MLEAF=1.00;MQ=63.50;MQ0=0;QD=37.18;RPA=24,29;RU=A;SB=-4.110e+02;STR	GT:AD:DP:GQ:PL	1/1:65,85:153:99:5688,340,0
chrXV	522811	.	G	GAA	1505.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=2.119;DP=199;FS=6.347;HaplotypeScore=485.8211;MLEAC=1;MLEAF=0.500;MQ=62.14;MQ0=0;MQRankSum=6.888;QD=7.57;RPA=28,30;RU=A;ReadPosRankSum=0.155;SB=-6.560e+02;STR	GT:AD:DP:GQ:PL	0/1:119,76:199:99:1545,0,877
chrXV	722778	.	T	TTC	2491.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-4.605;DP=192;FS=6.039;HaplotypeScore=96.5224;MLEAC=1;MLEAF=0.500;MQ=52.54;MQ0=0;MQRankSum=-9.793;QD=12.98;ReadPosRankSum=1.217;SB=-2.860e+02	GT:AD:DP:GQ:PL	0/1:129,62:192:99:2531,0,5789
chrXV	724940	.	GT	G	1253.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.128;DP=116;FS=1.534;HaplotypeScore=73.0036;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=0.787;QD=10.81;RPA=10,9;RU=T;ReadPosRankSum=-1.476;SB=-6.270e+02;STR	GT:AD:DP:GQ:PL	0/1:59,51:116:99:1293,0,1594
chrXVI	144689	.	AGGAAACGTC	A	16192	PASS	AC=2;AF=1.00;AN=2;DP=213;FS=0.000;HaplotypeScore=44.2629;MLEAC=2;MLEAF=1.00;MQ=41.28;MQ0=0;QD=76.02;RPA=4,3;RU=GGAAACGTC;SB=-4.484e+03;STR	GT:AD:DP:GQ:PL	1/1:60,152:213:99:16192,473,0
chrXVI	481304	.	AT	A	5246	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.104;DP=192;DS;FS=8.793;HaplotypeScore=66.4498;MLEAC=2;MLEAF=1.00;MQ=59.24;MQ0=0;MQRankSum=0.573;QD=27.32;RPA=13,12;RU=T;ReadPosRankSum=0.173;SB=-1.804e+03;STR	GT:AD:DP:GQ:PL	1/1:18,166:192:99:5246,466,0