##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/BY4742/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 21:36:26 PST 2014",Epoch=1389764186492,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/BY4742/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	BY4742
chrI	6736	.	C	CAA	318.96	PASS	AC=2;AF=1.00;AN=2;DP=35;FS=0.000;HaplotypeScore=9.3579;MLEAC=2;MLEAF=1.00;MQ=62.09;MQ0=0;QD=9.11;RPA=19,21;RU=A;SB=-2.200e+01;STR	GT:AD:DP:GQ:PL	1/1:23,12:35:36:361,36,0
chrI	19971	.	C	CCT	957.96	filter	AC=2;AF=1.00;AN=2;DP=44;FS=0.000;HaplotypeScore=11.4101;MLEAC=2;MLEAF=1.00;MQ=25.44;MQ0=11;QD=21.77;SB=-4.510e+02	GT:AD:DP:GQ:PL	1/1:1,41:20:60:1000,60,0
chrI	126880	.	C	CT,CTT	3977	PASS	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-1.704;DP=141;FS=0.000;HaplotypeScore=98.5653;MLEAC=1,1;MLEAF=0.500,0.500;MQ=64.98;MQ0=0;MQRankSum=1.366;QD=28.21;RPA=15,16,17;RU=T;ReadPosRankSum=0.944;SB=-9.691e+02;STR	GT:AD:DP:GQ:PL	1/2:23,6,112:141:52:3977,2084,1751,382,0,52
chrI	183387	.	AC	A	3065.96	PASS	AC=2;AF=1.00;AN=2;DP=85;FS=0.000;HaplotypeScore=13.5111;MLEAC=2;MLEAF=1.00;MQ=38.51;MQ0=1;QD=36.07;RPA=2,1;RU=C;SB=-1.019e+03;STR	GT:AD:DP:GQ:PL	1/1:1,84:76:99:3108,226,0
chrI	206176	.	CG	C	1395.96	PASS	AC=2;AF=1.00;AN=2;DP=37;FS=0.000;HaplotypeScore=255.7631;MLEAC=2;MLEAF=1.00;MQ=31.40;MQ0=2;QD=37.73;SB=-5.400e+02	GT:AD:DP:GQ:PL	1/1:16,21:33:99:1438,99,0
chrI	206179	.	A	AC	1394.96	PASS	AC=2;AF=1.00;AN=2;DP=40;FS=0.000;HaplotypeScore=266.5264;MLEAC=2;MLEAF=1.00;MQ=31.00;MQ0=2;QD=34.87;RPA=1,2;RU=C;SB=-5.270e+02;STR	GT:AD:DP:GQ:PL	1/1:19,21:36:99:1437,108,0
chrII	7912	.	GA	G	623.96	PASS	AC=2;AF=1.00;AN=2;DP=36;FS=0.000;HaplotypeScore=1.4973;MLEAC=2;MLEAF=1.00;MQ=23.61;MQ0=2;QD=17.33;RPA=3,2;RU=A;SB=-2.500e+02;STR	GT:AD:DP:GQ:PL	1/1:7,29:23:48:666,48,0
chrII	88484	.	GGAGAA	G	6942	PASS	AC=2;AF=1.00;AN=2;DP=99;FS=0.000;HaplotypeScore=11.8808;MLEAC=2;MLEAF=1.00;MQ=50.91;MQ0=0;QD=70.12;RPA=2,1;RU=GAGAA;SB=-1.914e+03;STR	GT:AD:DP:GQ:PL	1/1:9,90:99:99:6942,271,0
chrII	167978	.	C	CAA,CA	913.94	PASS	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-1.029;DP=61;FS=0.000;HaplotypeScore=29.9249;MLEAC=1,1;MLEAF=0.500,0.500;MQ=63.01;MQ0=0;MQRankSum=1.949;QD=14.98;RPA=16,18,17;RU=A;ReadPosRankSum=0.433;SB=-1.280e+02;STR	GT:AD:DP:GQ:PL	1/2:25,6,29:61:99:992,213,232,178,0,156
chrII	221288	.	AGT	A	820.96	PASS	AC=2;AF=1.00;AN=2;DP=22;FS=0.000;HaplotypeScore=1.0482;MLEAC=2;MLEAF=1.00;MQ=30.79;MQ0=1;QD=37.32;RPA=2,1;RU=GT;SB=-1.860e+02;STR	GT:AD:DP:GQ:PL	1/1:1,21:19:57:863,57,0
chrII	263158	.	CG	C	293.99	PASS	AC=2;AF=1.00;AN=2;DP=11;FS=0.000;HaplotypeScore=53.3915;MLEAC=2;MLEAF=1.00;MQ=31.33;MQ0=0;QD=26.73;RPA=2,1;RU=G;SB=-4.297e+01;STR	GT:AD:DP:GQ:PL	1/1:0,11:8:24:336,24,0
chrII	263168	.	CG	C	675.96	PASS	AC=2;AF=1.00;AN=2;DP=19;FS=0.000;HaplotypeScore=51.1831;MLEAC=2;MLEAF=1.00;MQ=40.35;MQ0=0;QD=35.58;SB=-3.250e+02	GT:AD:DP:GQ:PL	1/1:0,19:16:48:718,48,0
chrII	296125	.	A	AT	114.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.488;DP=72;FS=9.074;HaplotypeScore=130.2498;MLEAC=1;MLEAF=0.500;MQ=58.16;MQ0=0;MQRankSum=1.286;QD=1.60;RPA=22,23;RU=T;ReadPosRankSum=1.611;SB=-7.400e+01;STR	GT:AD:DP:GQ:PL	0/1:50,9:72:99:154,0,447
chrII	383176	.	C	CG	3195.96	PASS	AC=2;AF=1.00;AN=2;DP=80;FS=0.000;HaplotypeScore=16.3523;MLEAC=2;MLEAF=1.00;MQ=60.39;MQ0=0;QD=39.95;RPA=2,3;RU=G;SB=-9.490e+02;STR	GT:AD:DP:GQ:PL	1/1:1,77:80:99:3238,234,0
chrII	389425	.	TC	T	1907.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=2.917;DP=65;FS=23.590;HaplotypeScore=511.9702;MLEAC=2;MLEAF=1.00;MQ=49.08;MQ0=0;MQRankSum=1.560;QD=29.35;ReadPosRankSum=3.607;SB=-6.580e+02	GT:AD:DP:GQ:PL	1/1:9,49:65:99:1950,127,0
chrII	389429	.	CG	C	2134.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.559;DP=62;FS=3.310;HaplotypeScore=494.8045;MLEAC=2;MLEAF=1.00;MQ=49.85;MQ0=0;MQRankSum=0.346;QD=34.43;ReadPosRankSum=0.751;SB=-9.510e+02	GT:AD:DP:GQ:PL	1/1:11,49:62:99:2177,161,0
chrII	470235	.	A	AG	272.03	filter	AC=2;AF=1.00;AN=2;DP=7;FS=0.000;HaplotypeScore=136.0111;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=38.86;SB=-8.144e-04	GT:AD:DP:GQ:PL	1/1:0,7:7:21:314,21,0
chrII	470242	.	T	TC	269.03	filter	AC=2;AF=1.00;AN=2;DP=7;FS=0.000;HaplotypeScore=136.3700;MLEAC=2;MLEAF=1.00;MQ=29.00;MQ0=0;QD=38.43;SB=-8.144e-04	GT:AD:DP:GQ:PL	1/1:0,7:7:21:311,21,0
chrII	474238	.	GA	G	2137.96	PASS	AC=2;AF=1.00;AN=2;DP=56;FS=0.000;HaplotypeScore=369.6265;MLEAC=2;MLEAF=1.00;MQ=33.31;MQ0=0;QD=38.18;RPA=4,3;RU=A;SB=-7.050e+02;STR	GT:AD:DP:GQ:PL	1/1:2,54:56:99:2180,166,0
chrII	698075	.	G	GA	425.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=91;FS=3.914;HaplotypeScore=383.7687;MLEAC=1;MLEAF=0.500;MQ=56.72;MQ0=0;MQRankSum=-0.545;QD=4.68;RPA=17,18;RU=A;ReadPosRankSum=-2.060;SB=-8.400e+01;STR	GT:AD:DP:GQ:PL	0/1:64,26:91:99:465,0,899
chrII	723663	.	C	CA	1117.48	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.479;DP=69;FS=1.957;HaplotypeScore=56.5030;MLEAC=2;MLEAF=1.00;MQ=62.50;MQ0=0;MQRankSum=1.007;QD=16.20;RPA=15,16;RU=A;ReadPosRankSum=-0.347;SB=-4.263e+02;STR	GT:AD:DP:GQ:PL	1/1:23,44:69:12:1159,12,0
chrII	746362	.	CATCTGCA	C	7339	PASS	AC=2;AF=1.00;AN=2;DP=86;FS=0.000;HaplotypeScore=11.7898;MLEAC=2;MLEAF=1.00;MQ=60.11;MQ0=0;QD=85.34;RPA=2,1;RU=ATCTGCA;SB=-3.375e+03;STR	GT:AD:DP:GQ:PL	1/1:8,77:86:99:7339,235,0
chrIII	184	.	A	AC	224.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=32;FS=0.000;HaplotypeScore=177.8342;MLEAC=1;MLEAF=0.500;MQ=25.55;MQ0=3;MQRankSum=-0.453;QD=7.03;RPA=2,3;RU=C;ReadPosRankSum=1.087;SB=-8.600e+01;STR	GT:AD:DP:GQ:PL	0/1:24,7:19:99:264,0,219
chrIII	27658	.	T	TAA	547.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.638;DP=88;FS=5.786;HaplotypeScore=192.7004;MLEAC=1;MLEAF=0.500;MQ=62.43;MQ0=0;MQRankSum=3.804;QD=6.23;RPA=23,25;RU=A;ReadPosRankSum=0.311;SB=-1.320e+02;STR	GT:AD:DP:GQ:PL	0/1:58,28:88:99:587,0,178
chrIII	162712	.	TA	T	1648.96	PASS	AC=2;AF=1.00;AN=2;DP=51;FS=0.000;HaplotypeScore=199.9905;MLEAC=2;MLEAF=1.00;MQ=59.91;MQ0=0;QD=32.33;RPA=10,9;RU=A;SB=-5.310e+02;STR	GT:AD:DP:GQ:PL	1/1:0,51:51:99:1691,153,0
chrIII	163163	.	G	GA	2482.96	PASS	AC=2;AF=1.00;AN=2;DP=81;FS=0.000;HaplotypeScore=262.6395;MLEAC=2;MLEAF=1.00;MQ=59.14;MQ0=0;QD=30.65;RPA=9,10;RU=A;SB=-1.169e+03;STR	GT:AD:DP:GQ:PL	1/1:6,71:81:99:2525,228,0
chrIII	163192	.	A	AT	2591.96	PASS	AC=2;AF=1.00;AN=2;DP=72;FS=0.000;HaplotypeScore=236.4473;MLEAC=2;MLEAF=1.00;MQ=59.98;MQ0=0;QD=36.00;RPA=3,4;RU=T;SB=-9.620e+02;STR	GT:AD:DP:GQ:PL	1/1:4,68:72:99:2634,205,0
chrIV	135456	.	CT	C	118.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.024;DP=41;FS=0.000;HaplotypeScore=34.6605;MLEAC=1;MLEAF=0.500;MQ=60.53;MQ0=0;MQRankSum=1.683;QD=2.90;RPA=18,17;RU=T;ReadPosRankSum=0.415;SB=-1.800e+01;STR	GT:AD:DP:GQ:PL	0/1:30,8:41:99:158,0,475
chrIV	344004	.	G	GTA	794.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.481;DP=74;FS=0.000;HaplotypeScore=54.9684;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-1.614;QD=10.74;RPA=13,14;RU=TA;ReadPosRankSum=-0.275;SB=-3.990e+02;STR	GT:AD:DP:GQ:PL	0/1:55,14:74:99:834,0,276
chrIV	403511	.	G	GT	3085.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.476;DP=92;FS=3.793;HaplotypeScore=11.1115;MLEAC=2;MLEAF=1.00;MQ=61.86;MQ0=0;MQRankSum=-0.095;QD=33.54;RPA=9,10;RU=T;ReadPosRankSum=-0.133;SB=-1.241e+03;STR	GT:AD:DP:GQ:PL	1/1:1,90:92:99:3128,240,0
chrIV	548546	.	G	GT	444.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.399;DP=59;FS=17.035;HaplotypeScore=127.1002;MLEAC=1;MLEAF=0.500;MQ=61.16;MQ0=0;MQRankSum=2.493;QD=7.54;RPA=19,20;RU=T;ReadPosRankSum=-2.557;SB=-1.640e+02;STR	GT:AD:DP:GQ:PL	0/1:27,23:59:89:484,0,89
chrIV	678013	.	C	CTT	432.96	PASS	AC=2;AF=1.00;AN=2;DP=35;FS=0.000;HaplotypeScore=23.8261;MLEAC=2;MLEAF=1.00;MQ=64.19;MQ0=0;QD=12.37;RPA=35,37;RU=T;SB=-2.000e+01;STR	GT:AD:DP:GQ:PL	1/1:19,15:35:48:475,48,0
chrIV	688062	.	C	CTTT,CTT	2147.95	PASS	AC=1,1;AF=0.500,0.500;AN=2;DP=77;FS=0.000;HaplotypeScore=60.6992;MLEAC=1,1;MLEAF=0.500,0.500;MQ=61.72;MQ0=0;QD=27.90;RPA=14,17,16;RU=T;SB=-9.860e+02;STR	GT:AD:DP:GQ:PL	1/2:15,5,50:77:81:2226,917,796,254,0,81
chrIV	817531	.	T	TA	1913.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.775;DP=83;FS=8.083;HaplotypeScore=27.9572;MLEAC=2;MLEAF=1.00;MQ=60.49;MQ0=0;MQRankSum=-1.151;QD=23.06;RPA=10,11;RU=A;ReadPosRankSum=-0.564;SB=-7.920e+02;STR	GT:AD:DP:GQ:PL	1/1:19,62:83:39:1956,39,0
chrIV	1079010	.	AT	A	249.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.666;DP=60;FS=6.046;HaplotypeScore=69.7480;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.897;QD=4.17;RPA=20,19;RU=T;ReadPosRankSum=0.415;SB=-1.330e+02;STR	GT:AD:DP:GQ:PL	0/1:44,8:60:99:289,0,708
chrIV	1150910	.	A	AG	2074.96	PASS	AC=2;AF=1.00;AN=2;DP=56;FS=0.000;HaplotypeScore=10.3605;MLEAC=2;MLEAF=1.00;MQ=54.37;MQ0=0;QD=37.05;RPA=2,3;RU=G;SB=-1.050e+03;STR	GT:AD:DP:GQ:PL	1/1:3,53:53:99:2117,151,0
chrIV	1305680	.	TG	T	3543	PASS	AC=2;AF=1.00;AN=2;DP=90;FS=0.000;HaplotypeScore=7.1279;MLEAC=2;MLEAF=1.00;MQ=60.72;MQ0=0;QD=39.37;RPA=2,1;RU=G;SB=-1.488e+03;STR	GT:AD:DP:GQ:PL	1/1:0,84:90:99:3543,253,0
chrIV	1515034	.	TA	T	2297.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.732;DP=76;FS=0.000;HaplotypeScore=23.6496;MLEAC=2;MLEAF=1.00;MQ=59.20;MQ0=0;MQRankSum=1.685;QD=30.24;RPA=11,10;RU=A;ReadPosRankSum=1.592;SB=-1.034e+03;STR	GT:AD:DP:GQ:PL	1/1:3,71:76:99:2340,200,0
chrIV	1518948	.	G	GT	1631.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=1.190;DP=68;FS=0.000;HaplotypeScore=34.7908;MLEAC=1;MLEAF=0.500;MQ=60.46;MQ0=0;MQRankSum=-0.466;QD=24.00;RPA=13,14;RU=T;ReadPosRankSum=-1.363;SB=-4.909e+02;STR	GT:AD:DP:GQ:PL	1/1:13,50:68:81:1674,81,0
chrIV	1525376	.	TG	T	1347.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=4.307;DP=67;FS=59.203;HaplotypeScore=2232.5375;MLEAC=1;MLEAF=0.500;MQ=27.60;MQ0=0;MQRankSum=1.010;QD=20.12;RPA=3,2;RU=G;ReadPosRankSum=3.378;SB=-3.011e+00;STR	GT:AD:DP:GQ:PL	0/1:29,33:61:99:1387,0,137
chrIV	1525391	.	GT	G	1142.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=5.226;DP=70;FS=40.848;HaplotypeScore=1926.2394;MLEAC=1;MLEAF=0.500;MQ=27.78;MQ0=1;MQRankSum=-0.898;QD=16.33;ReadPosRankSum=2.944;SB=-8.144e-04	GT:AD:DP:GQ:PL	0/1:41,24:62:99:1182,0,564
chrIX	39373	.	T	TA	2622.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=1.640;DP=98;FS=0.000;HaplotypeScore=53.1171;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;MQRankSum=-0.081;QD=26.76;RPA=11,12;RU=A;ReadPosRankSum=-1.314;SB=-7.690e+02;STR	GT:AD:DP:GQ:PL	1/1:10,81:98:99:2665,159,0
chrIX	57277	.	C	CA	619.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.470;DP=56;FS=13.497;HaplotypeScore=39.7389;MLEAC=1;MLEAF=0.500;MQ=63.09;MQ0=0;MQRankSum=2.357;QD=11.07;RPA=16,17;RU=A;ReadPosRankSum=-0.677;SB=-2.750e+02;STR	GT:AD:DP:GQ:PL	0/1:27,28:56:60:659,0,60
chrIX	105433	.	A	AAAT	2506.96	PASS	AC=2;AF=1.00;AN=2;DP=48;FS=0.000;HaplotypeScore=10.1686;MLEAC=2;MLEAF=1.00;MQ=61.56;MQ0=0;QD=52.23;RPA=3,4;RU=AAT;SB=-1.082e+03;STR	GT:AD:DP:GQ:PL	1/1:2,46:48:99:2549,138,0
chrIX	241032	.	G	GAA	664.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.394;DP=64;FS=0.000;HaplotypeScore=146.7106;MLEAC=1;MLEAF=0.500;MQ=63.77;MQ0=0;MQRankSum=5.036;QD=10.39;RPA=21,23;RU=A;ReadPosRankSum=0.671;SB=-2.300e+01;STR	GT:AD:DP:GQ:PL	0/1:31,32:64:99:704,0,104
chrIX	254003	.	TA	T	1614.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.681;DP=101;FS=0.000;HaplotypeScore=56.3326;MLEAC=2;MLEAF=1.00;MQ=59.60;MQ0=0;MQRankSum=-1.547;QD=15.99;RPA=15,14;RU=A;ReadPosRankSum=1.670;SB=-6.158e+02;STR	GT:AD:DP:GQ:PL	1/1:33,51:101:99:1657,133,0
chrM	20345	.	GA	G	8135	PASS	AC=2;AF=1.00;AN=2;DP=250;DS;FS=0.000;HaplotypeScore=79.5797;MLEAC=2;MLEAF=1.00;MQ=60.64;MQ0=0;QD=32.54;RPA=3,2;RU=A;SB=-2.702e+03;STR	GT:AD:DP:GQ:PL	1/1:0,250:250:99:8135,752,0
chrM	33618	.	T	TTC	1753.96	PASS	AC=2;AF=1.00;AN=2;DP=38;FS=0.000;HaplotypeScore=2.5977;MLEAC=2;MLEAF=1.00;MQ=60.44;MQ0=0;QD=46.16;SB=-2.500e+02	GT:AD:DP:GQ:PL	1/1:0,37:37:99:1796,111,0
chrM	33793	.	C	CG	600.96	PASS	AC=2;AF=1.00;AN=2;DP=23;FS=0.000;HaplotypeScore=30.9801;MLEAC=2;MLEAF=1.00;MQ=55.24;MQ0=0;QD=26.13;RPA=7,8;RU=G;SB=-1.780e+02;STR	GT:AD:DP:GQ:PL	1/1:1,22:23:66:643,66,0
chrM	43084	.	A	AT	1446.96	PASS	AC=2;AF=1.00;AN=2;DP=51;FS=0.000;HaplotypeScore=21.6491;MLEAC=2;MLEAF=1.00;MQ=60.19;MQ0=0;QD=28.37;RPA=8,9;RU=T;SB=-3.320e+02;STR	GT:AD:DP:GQ:PL	1/1:2,49:51:99:1489,150,0
chrM	44795	.	A	AT	531.96	PASS	AC=2;AF=1.00;AN=2;DP=23;FS=0.000;HaplotypeScore=7.3559;MLEAC=2;MLEAF=1.00;MQ=55.12;MQ0=0;QD=23.13;RPA=8,9;RU=T;SB=-2.380e+02;STR	GT:AD:DP:GQ:PL	1/1:2,20:22:57:574,57,0
chrM	63582	.	TTAAGTA	T	921.96	PASS	AC=2;AF=1.00;AN=2;DP=53;FS=0.000;HaplotypeScore=14.2484;MLEAC=2;MLEAF=1.00;MQ=60.29;MQ0=0;QD=17.40;RPA=11,10;RU=TAAGTA;SB=-1.440e+02;STR	GT:AD:DP:GQ:PL	1/1:37,16:53:51:964,51,0
chrM	65917	.	CG	C	925.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.096;DP=42;FS=0.000;HaplotypeScore=31.1885;MLEAC=2;MLEAF=1.00;MQ=56.54;MQ0=0;MQRankSum=1.059;QD=22.05;RPA=9,8;RU=G;ReadPosRankSum=-1.348;SB=-1.450e+02;STR	GT:AD:DP:GQ:PL	1/1:7,35:42:79:968,79,0
chrM	67400	.	T	TC	2366.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.140;DP=103;FS=0.000;HaplotypeScore=66.4609;MLEAC=2;MLEAF=1.00;MQ=60.21;MQ0=0;MQRankSum=1.010;QD=22.98;RPA=9,10;RU=C;ReadPosRankSum=0.269;SB=-4.940e+02;STR	GT:AD:DP:GQ:PL	1/1:11,87:103:99:2409,190,0
chrM	73114	.	AG	A	1004.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.733;DP=40;FS=0.000;HaplotypeScore=101.0824;MLEAC=2;MLEAF=1.00;MQ=57.28;MQ0=0;MQRankSum=1.636;QD=25.12;RPA=6,5;RU=G;ReadPosRankSum=0.674;SB=-2.850e+02;STR	GT:AD:DP:GQ:PL	1/1:3,35:40:76:1047,76,0
chrM	73136	.	TC	T	894.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.255;DP=29;FS=0.000;HaplotypeScore=181.8998;MLEAC=2;MLEAF=1.00;MQ=53.62;MQ0=0;MQRankSum=1.135;QD=30.86;RPA=3,2;RU=C;ReadPosRankSum=1.016;SB=-2.080e+02;STR	GT:AD:DP:GQ:PL	1/1:4,25:29:59:937,59,0
chrV	272558	.	GT	G	1932.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.178;DP=76;FS=3.078;HaplotypeScore=33.6338;MLEAC=2;MLEAF=1.00;MQ=59.95;MQ0=0;MQRankSum=0.393;QD=25.43;RPA=12,11;RU=T;ReadPosRankSum=1.328;SB=-9.240e+02;STR	GT:AD:DP:GQ:PL	1/1:12,61:76:99:1975,141,0
chrVI	4740	.	A	ACAC	549.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.001;DP=52;FS=0.000;HaplotypeScore=336.0727;MLEAC=1;MLEAF=0.500;MQ=40.70;MQ0=5;MQRankSum=-1.828;QD=10.58;ReadPosRankSum=0.360;SB=-2.630e+02	GT:AD:DP:GQ:PL	0/1:38,11:44:99:589,0,953
chrVI	11068	.	CT	C	1178.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.091;DP=130;FS=6.516;HaplotypeScore=77.8280;MLEAC=1;MLEAF=0.500;MQ=43.55;MQ0=1;MQRankSum=-3.024;QD=9.07;RPA=14,13;RU=T;ReadPosRankSum=0.882;SB=-3.470e+02;STR	GT:AD:DP:GQ:PL	0/1:79,49:127:99:1218,0,1460
chrVI	97864	.	C	CTT	3079.96	PASS	AC=2;AF=1.00;AN=2;DP=80;FS=0.000;HaplotypeScore=75.3164;MLEAC=2;MLEAF=1.00;MQ=60.16;MQ0=0;QD=38.50;RPA=10,12;RU=T;SB=-9.050e+02;STR	GT:AD:DP:GQ:PL	1/1:9,67:80:99:3122,214,0
chrVI	106277	.	C	CTT	2025.96	PASS	AC=2;AF=1.00;AN=2;DP=75;FS=0.000;HaplotypeScore=56.1949;MLEAC=2;MLEAF=1.00;MQ=66.59;MQ0=0;QD=27.01;RPA=13,15;RU=T;SB=-1.530e+02;STR	GT:AD:DP:GQ:PL	1/1:13,59:75:99:2068,186,0
chrVII	214	.	A	AC	797.96	PASS	AC=2;AF=1.00;AN=2;DP=25;FS=0.000;HaplotypeScore=2.2412;MLEAC=2;MLEAF=1.00;MQ=28.92;MQ0=1;QD=31.92;RPA=2,3;RU=C;SB=-3.360e+02;STR	GT:AD:DP:GQ:PL	1/1:2,23:22:60:840,60,0
chrVII	8151	.	G	GA	356.97	filter	AC=2;AF=1.00;AN=2;DP=26;FS=0.000;HaplotypeScore=1.2387;MLEAC=2;MLEAF=1.00;MQ=33.92;MQ0=14;QD=13.73;RPA=1,2;RU=A;SB=-1.099e+02;STR	GT:AD:DP:GQ:PL	1/1:0,26:10:30:399,30,0
chrVII	326269	.	CA	C	121.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.354;DP=52;FS=0.000;HaplotypeScore=81.7708;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.161;QD=2.35;RPA=18,17;RU=A;ReadPosRankSum=-0.193;SB=-6.900e+01;STR	GT:AD:DP:GQ:PL	0/1:37,7:52:99:161,0,637
chrVII	405085	.	CG	C	2884.96	PASS	AC=2;AF=1.00;AN=2;DP=78;FS=0.000;HaplotypeScore=9.3054;MLEAC=2;MLEAF=1.00;MQ=52.61;MQ0=0;QD=36.99;RPA=2,1;RU=G;SB=-5.070e+02;STR	GT:AD:DP:GQ:PL	1/1:0,77:69:99:2927,205,0
chrVII	496729	.	T	TA	1115.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.159;DP=50;FS=0.000;HaplotypeScore=30.9959;MLEAC=2;MLEAF=1.00;MQ=60.41;MQ0=0;MQRankSum=-0.732;QD=22.32;RPA=13,14;RU=A;ReadPosRankSum=-2.260;SB=-3.740e+02;STR	GT:AD:DP:GQ:PL	1/1:13,36:50:54:1158,54,0
chrVII	640641	.	TA	T	329.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.698;DP=74;FS=140.144;HaplotypeScore=105.9770;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=4.520;QD=4.46;ReadPosRankSum=-3.954;SB=-3.010e+00	GT:AD:DP:GQ:PL	0/1:54,20:73:99:369,0,1607
chrVII	733109	.	AT	A	446.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.561;DP=92;FS=0.000;HaplotypeScore=112.6105;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=0.620;QD=4.86;RPA=20,19;RU=T;ReadPosRankSum=0.126;SB=-1.680e+02;STR	GT:AD:DP:GQ:PL	0/1:65,17:92:99:486,0,1025
chrVIII	2292	.	G	GC	704.99	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.036;DP=44;FS=2.418;HaplotypeScore=40.4063;MLEAC=1;MLEAF=0.500;MQ=45.70;MQ0=0;MQRankSum=-0.537;QD=16.02;RPA=11,12;RU=C;ReadPosRankSum=-0.967;SB=-3.465e+02;STR	GT:AD:DP:GQ:PL	0/1:13,28:44:20:744,0,20
chrVIII	17534	.	A	AT	1667.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.710;DP=61;FS=2.800;HaplotypeScore=33.5790;MLEAC=2;MLEAF=1.00;MQ=59.62;MQ0=0;MQRankSum=-1.031;QD=27.34;RPA=11,12;RU=T;ReadPosRankSum=-0.389;SB=-6.550e+02;STR	GT:AD:DP:GQ:PL	1/1:10,50:61:99:1710,99,0
chrVIII	85508	.	TTA	T	3119.96	PASS	AC=2;AF=1.00;AN=2;DP=84;FS=0.000;HaplotypeScore=18.0759;MLEAC=2;MLEAF=1.00;MQ=49.09;MQ0=0;QD=37.14;RPA=4,3;RU=TA;SB=-1.483e+03;STR	GT:AD:DP:GQ:PL	1/1:14,69:82:99:3162,208,0
chrVIII	237735	.	C	CT	59.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.257;DP=49;FS=1.906;HaplotypeScore=55.0942;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.027;QD=1.22;RPA=16,17;RU=T;ReadPosRankSum=0.064;SB=-2.900e+01;STR	GT:AD:DP:GQ:PL	0/1:35,7:49:99:99,0,872
chrVIII	396945	.	GA	G	464.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.414;DP=58;FS=0.000;HaplotypeScore=98.9819;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=-1.032;QD=8.02;RPA=19,18;RU=A;ReadPosRankSum=0.078;SB=-2.030e+02;STR	GT:AD:DP:GQ:PL	0/1:33,15:58:99:504,0,443
chrVIII	475931	.	TTA	T	1114.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.839;DP=71;FS=0.000;HaplotypeScore=29.1518;MLEAC=2;MLEAF=1.00;MQ=61.19;MQ0=0;MQRankSum=-0.168;QD=15.70;RPA=11,10;RU=TA;ReadPosRankSum=1.621;SB=-5.580e+02;STR	GT:AD:DP:GQ:PL	1/1:40,29:71:50:1157,50,0
chrVIII	549799	.	TCA	T	281.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=4.067;DP=42;FS=82.868;HaplotypeScore=92.9793;MLEAC=1;MLEAF=0.500;MQ=32.60;MQ0=6;MQRankSum=1.394;QD=6.71;ReadPosRankSum=-3.800;SB=-3.007e+00	GT:AD:DP:GQ:PL	0/1:30,10:34:99:321,0,1085
chrVIII	562385	.	AT	A	300.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=0.439;DP=118;FS=16.542;HaplotypeScore=206.5473;MLEAC=1;MLEAF=0.500;MQ=25.47;MQ0=46;MQRankSum=2.440;QD=2.55;RPA=12,11;RU=T;ReadPosRankSum=-1.951;SB=-8.144e-04;STR	GT:AD:DP:GQ:PL	0/1:90,28:68:99:340,0,1367
chrX	470130	.	GTAA	G	1831.96	PASS	AC=2;AF=1.00;AN=2;DP=67;FS=0.000;HaplotypeScore=50.1656;MLEAC=2;MLEAF=1.00;MQ=60.42;MQ0=0;QD=27.34;RPA=16,15;RU=TAA;SB=-4.870e+02;STR	GT:AD:DP:GQ:PL	1/1:19,36:67:99:1874,123,0
chrX	550151	.	CT	C	90.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=0.742;DP=66;FS=2.813;HaplotypeScore=47.5344;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=-0.032;QD=1.38;RPA=13,12;RU=T;ReadPosRankSum=0.710;SB=-1.100e+01;STR	GT:AD:DP:GQ:PL	0/1:49,9:66:99:130,0,1503
chrX	640784	.	G	GA	1947.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.033;DP=65;FS=0.000;HaplotypeScore=15.2786;MLEAC=2;MLEAF=1.00;MQ=60.50;MQ0=0;MQRankSum=-0.787;QD=29.97;RPA=10,11;RU=A;ReadPosRankSum=0.722;SB=-6.020e+02;STR	GT:AD:DP:GQ:PL	1/1:6,59:65:86:1990,86,0
chrXI	457	.	C	CA	2253.96	PASS	AC=2;AF=1.00;AN=2;DP=49;FS=0.000;HaplotypeScore=9.5307;MLEAC=2;MLEAF=1.00;MQ=59.31;MQ0=0;QD=46.00;SB=-1.090e+03	GT:AD:DP:GQ:PL	1/1:0,49:49:99:2296,148,0
chrXI	68454	.	G	GCC	3227.04	PASS	AC=2;AF=1.00;AN=2;DP=58;FS=0.000;HaplotypeScore=232.7570;MLEAC=2;MLEAF=1.00;MQ=56.74;MQ0=0;QD=55.64;SB=-1.520e+03	GT:AD:DP:GQ:PL	1/1:4,54:58:99:3269,175,0
chrXI	68468	.	T	TG	3313	PASS	AC=2;AF=1.00;AN=2;DP=70;FS=0.000;HaplotypeScore=275.1494;MLEAC=2;MLEAF=1.00;MQ=57.31;MQ0=0;QD=47.33;SB=-1.510e+03	GT:AD:DP:GQ:PL	1/1:0,70:70:99:3313,211,0
chrXI	451568	.	GGAACAC	G	6618	PASS	AC=2;AF=1.00;AN=2;DP=87;FS=0.000;HaplotypeScore=12.1365;MLEAC=2;MLEAF=1.00;MQ=60.19;MQ0=0;QD=76.07;RPA=2,1;RU=GAACAC;SB=-3.110e+03;STR	GT:AD:DP:GQ:PL	1/1:10,77:87:99:6618,232,0
chrXI	666556	.	GT	G	2266.96	PASS	AC=2;AF=1.00;AN=2;DP=50;FS=0.000;HaplotypeScore=34.5950;MLEAC=2;MLEAF=1.00;MQ=55.26;MQ0=0;QD=45.34;SB=-4.590e+02	GT:AD:DP:GQ:PL	1/1:1,49:50:99:2309,147,0
chrXI	666642	.	G	GGT	536.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=0.826;DP=53;FS=6.593;HaplotypeScore=297.5406;MLEAC=1;MLEAF=0.500;MQ=32.24;MQ0=6;MQRankSum=0.106;QD=10.13;RPA=2,3;RU=GT;ReadPosRankSum=1.164;SB=-8.144e-04;STR	GT:AD:DP:GQ:PL	0/1:43,8:36:99:576,0,341
chrXII	552	.	AT	A	507.96	filter	AC=2;AF=1.00;AN=2;DP=14;FS=0.000;HaplotypeScore=35.3521;MLEAC=2;MLEAF=1.00;MQ=24.37;MQ0=1;QD=36.28;RPA=2,1;RU=T;SB=-8.144e-04;STR	GT:AD:DP:GQ:PL	1/1:0,13:13:39:550,39,0
chrXII	591	.	T	TGTACAGC	968.96	filter	AC=2;AF=1.00;AN=2;DP=13;FS=0.000;HaplotypeScore=47.3324;MLEAC=2;MLEAF=1.00;MQ=25.29;MQ0=0;QD=74.54;SB=-8.144e-04	GT:AD:DP:GQ:PL	1/1:7,6:13:39:1011,39,0
chrXII	11195	.	TAC	T	898.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.246;DP=121;FS=3.393;HaplotypeScore=317.9194;MLEAC=1;MLEAF=0.500;MQ=34.52;MQ0=40;MQRankSum=-2.725;QD=7.43;RPA=2,1;RU=AC;ReadPosRankSum=1.109;SB=-2.120e+02;STR	GT:AD:DP:GQ:PL	0/1:90,25:81:99:938,0,2329
chrXII	11225	.	CA	C	2281.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.551;DP=102;FS=7.886;HaplotypeScore=327.2173;MLEAC=1;MLEAF=0.500;MQ=42.07;MQ0=2;MQRankSum=3.465;QD=22.37;ReadPosRankSum=3.502;SB=-1.053e+03	GT:AD:DP:GQ:PL	0/1:34,60:97:99:2321,0,828
chrXII	187137	.	AT	A	4702	PASS	AC=2;AF=1.00;AN=2;DP=119;FS=0.000;HaplotypeScore=13.9795;MLEAC=2;MLEAF=1.00;MQ=59.70;MQ0=0;QD=39.51;RPA=3,2;RU=T;SB=-9.750e+02;STR	GT:AD:DP:GQ:PL	1/1:2,117:119:99:4702,352,0
chrXII	421496	.	AG	A	148.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.656;DP=25;FS=3.424;HaplotypeScore=24.8124;MLEAC=1;MLEAF=0.500;MQ=54.62;MQ0=0;MQRankSum=1.369;QD=5.96;RPA=11,10;RU=G;ReadPosRankSum=-0.377;SB=-1.900e+01;STR	GT:AD:DP:GQ:PL	0/1:16,7:25:99:188,0,133
chrXII	784382	.	G	GC	3656	PASS	AC=2;AF=1.00;AN=2;DP=98;FS=0.000;HaplotypeScore=13.3527;MLEAC=2;MLEAF=1.00;MQ=59.30;MQ0=0;QD=37.31;RPA=2,3;RU=C;SB=-1.246e+03;STR	GT:AD:DP:GQ:PL	1/1:2,95:97:99:3656,283,0
chrXII	881947	.	C	CAT	742.01	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=1.073;DP=53;FS=0.000;HaplotypeScore=16.0505;MLEAC=2;MLEAF=1.00;MQ=61.11;MQ0=2;MQRankSum=1.073;QD=14.00;RPA=11,12;RU=AT;ReadPosRankSum=-0.083;SB=-1.996e+02;STR	GT:AD:DP:GQ:PL	1/1:26,23:51:22:784,22,0
chrXII	1012324	.	C	CG	1970.96	PASS	AC=2;AF=1.00;AN=2;DP=55;FS=0.000;HaplotypeScore=247.4569;MLEAC=2;MLEAF=1.00;MQ=52.89;MQ0=0;QD=35.84;RPA=1,2;RU=G;SB=-5.990e+02;STR	GT:AD:DP:GQ:PL	1/1:11,44:55:99:2013,156,0
chrXII	1012328	.	A	AGCC	2543.96	PASS	AC=2;AF=1.00;AN=2;DP=49;FS=0.000;HaplotypeScore=193.2477;MLEAC=2;MLEAF=1.00;MQ=52.21;MQ0=0;QD=51.92;RPA=1,2;RU=GCC;SB=-3.410e+02;STR	GT:AD:DP:GQ:PL	1/1:4,45:49:99:2586,138,0
chrXIII	164392	.	G	GT	256.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.806;DP=56;FS=5.180;HaplotypeScore=62.5463;MLEAC=1;MLEAF=0.500;MQ=62.83;MQ0=0;MQRankSum=3.644;QD=4.59;RPA=25,26;RU=T;ReadPosRankSum=1.806;SB=-7.888e+01;STR	GT:AD:DP:GQ:PL	0/1:39,16:56:97:296,0,97
chrXIII	698679	.	TA	T	173.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.603;DP=76;FS=0.000;HaplotypeScore=59.3425;MLEAC=1;MLEAF=0.500;MQ=58.35;MQ0=0;MQRankSum=0.152;QD=2.29;RPA=17,16;RU=A;ReadPosRankSum=0.823;SB=-7.300e+01;STR	GT:AD:DP:GQ:PL	0/1:55,14:76:99:213,0,1575
chrXIII	908558	.	T	TCAA	2095.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.518;DP=202;DS;FS=2.169;HaplotypeScore=950.2356;MLEAC=1;MLEAF=0.500;MQ=49.85;MQ0=1;MQRankSum=0.416;QD=10.38;RPA=1,2;RU=CAA;ReadPosRankSum=-1.524;SB=-9.210e+02;STR	GT:AD:DP:GQ:PL	0/1:148,50:181:99:2135,0,6778
chrXIII	918120	.	C	CT	269.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.364;DP=39;FS=0.000;HaplotypeScore=38.0513;MLEAC=1;MLEAF=0.500;MQ=55.19;MQ0=1;MQRankSum=2.322;QD=6.92;RPA=19,20;RU=T;ReadPosRankSum=-3.059;SB=-7.600e+01;STR	GT:AD:DP:GQ:PL	0/1:14,17:38:76:309,0,76
chrXIII	921418	.	CT	C	678.99	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.760;DP=36;FS=5.539;HaplotypeScore=51.5388;MLEAC=2;MLEAF=1.00;MQ=38.56;MQ0=1;MQRankSum=2.558;QD=18.86;RPA=14,13;RU=T;ReadPosRankSum=0.760;SB=-3.238e+02;STR	GT:AD:DP:GQ:PL	1/1:14,20:34:24:721,24,0
chrXIV	6636	.	CA	C	1282.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.775;DP=85;FS=14.467;HaplotypeScore=491.9571;MLEAC=1;MLEAF=0.500;MQ=32.43;MQ0=5;MQRankSum=0.341;QD=15.09;ReadPosRankSum=3.141;SB=-3.200e+02	GT:AD:DP:GQ:PL	0/1:49,32:67:99:1322,0,404
chrXIV	7478	.	A	AT	1152.96	filter	AC=2;AF=1.00;AN=2;DP=50;FS=0.000;HaplotypeScore=10.4468;MLEAC=2;MLEAF=1.00;MQ=23.90;MQ0=10;QD=23.06;SB=-1.890e+02	GT:AD:DP:GQ:PL	1/1:2,47:27:78:1195,78,0
chrXIV	312328	.	AACG	A	4773	PASS	AC=2;AF=1.00;AN=2;DP=93;FS=0.000;HaplotypeScore=11.6923;MLEAC=2;MLEAF=1.00;MQ=61.04;MQ0=0;QD=51.32;RPA=3,2;RU=ACG;SB=-2.204e+03;STR	GT:AD:DP:GQ:PL	1/1:9,84:93:99:4773,253,0
chrXIV	439397	.	G	GT	2476.96	PASS	AC=2;AF=1.00;AN=2;DP=74;FS=0.000;HaplotypeScore=5.7549;MLEAC=2;MLEAF=1.00;MQ=60.95;MQ0=1;QD=33.47;RPA=6,7;RU=T;SB=-9.480e+02;STR	GT:AD:DP:GQ:PL	1/1:6,68:73:99:2519,202,0
chrXIV	651857	.	AT	A	122.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.178;DP=44;FS=0.000;HaplotypeScore=47.1213;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=1.045;QD=2.79;RPA=17,16;RU=T;ReadPosRankSum=0.146;SB=-7.683e+01;STR	GT:AD:DP:GQ:PL	0/1:30,8:44:99:162,0,814
chrXIV	777553	.	AAT	A	204.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.148;DP=39;FS=1.957;HaplotypeScore=28.3031;MLEAC=1;MLEAF=0.500;MQ=60.28;MQ0=0;MQRankSum=-1.236;QD=5.26;RPA=13,12;RU=AT;ReadPosRankSum=-2.119;SB=-1.160e+02;STR	GT:AD:DP:GQ:PL	0/1:29,6:39:99:244,0,299
chrXIV	784151	.	GT	G	180.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=2.532;DP=30;FS=29.783;HaplotypeScore=276.5671;MLEAC=1;MLEAF=0.500;MQ=24.99;MQ0=1;MQRankSum=-0.489;QD=6.03;ReadPosRankSum=2.355;SB=-8.138e-04	GT:AD:DP:GQ:PL	0/1:20,10:18:99:220,0,307
chrXIV	784163	.	T	TG	291.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=1.893;DP=32;FS=0.000;HaplotypeScore=285.4674;MLEAC=1;MLEAF=0.500;MQ=23.95;MQ0=2;MQRankSum=-0.979;QD=9.12;RPA=2,3;RU=G;ReadPosRankSum=0.065;SB=-4.000e+01;STR	GT:AD:DP:GQ:PL	0/1:20,11:18:79:331,0,79
chrXIV	784235	.	GT	G	230.97	filter	AC=1;AF=0.500;AN=2;BaseQRankSum=1.107;DP=25;FS=10.843;HaplotypeScore=273.3021;MLEAC=1;MLEAF=0.500;MQ=27.76;MQ0=2;MQRankSum=0.241;QD=9.24;ReadPosRankSum=2.454;SB=-8.144e-04	GT:AD:DP:GQ:PL	0/1:19,6:17:99:270,0,143
chrXIV	784239	.	GT	G	161.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.318;DP=25;FS=0.000;HaplotypeScore=280.5540;MLEAC=1;MLEAF=0.500;MQ=27.76;MQ0=2;MQRankSum=1.059;QD=6.48;ReadPosRankSum=1.059;SB=-1.900e+01	GT:AD:DP:GQ:PL	0/1:19,5:17:99:201,0,185
chrXV	882623	.	C	CT	391.97	PASS	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.117;DP=104;FS=31.827;HaplotypeScore=297.9426;MLEAC=1;MLEAF=0.500;MQ=60.28;MQ0=0;MQRankSum=3.762;QD=3.77;RPA=20,21;RU=T;ReadPosRankSum=0.574;SB=-1.820e+02;STR	GT:AD:DP:GQ:PL	0/1:73,25:104:99:431,0,529
chrXVI	144689	.	AGGAAACGTC	A	7085	PASS	AC=2;AF=1.00;AN=2;DP=82;FS=0.000;HaplotypeScore=14.6764;MLEAC=2;MLEAF=1.00;MQ=37.96;MQ0=0;QD=86.40;RPA=4,3;RU=GGAAACGTC;SB=-1.269e+03;STR	GT:AD:DP:GQ:PL	1/1:18,64:82:99:7085,199,0
chrXVI	481304	.	AT	A	2299.96	PASS	AC=2;AF=1.00;AN=2;BaseQRankSum=0.263;DP=89;FS=6.219;HaplotypeScore=57.8921;MLEAC=2;MLEAF=1.00;MQ=59.79;MQ0=0;MQRankSum=-1.397;QD=25.84;RPA=13,12;RU=T;ReadPosRankSum=0.305;SB=-5.050e+02;STR	GT:AD:DP:GQ:PL	1/1:9,77:89:99:2342,109,0