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##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##GATKCommandLine=<ID=UnifiedGenotyper,Version=3.3-0-g37228af,Date="Tue May 19 17:32:21 CEST 2015",Epoch=1432049541721,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[122_S21_ORDERED_REALIGNED_RECAL.bam] showFullBamList=false 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=/home/mondino/../../media/mondino/Seagate Expansion Drive/Backup 17 11 14/Reference_genome/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=5000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 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 genotype_likelihoods_model=BOTH pcr_error_rate=1.0E-4 computeSLOD=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
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##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
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##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
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##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
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##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
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##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
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#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	48_2
13	110802745	.	C	T	4868.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=10.252;DP=5000;Dels=0.00;FS=34.851;HaplotypeScore=273.5558;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-33.793;QD=0.97;ReadPosRankSum=-23.812;SOR=7.569	GT:AD:DP:GQ:PL	0/1:4551,447:5000:99:4897,0,54514
13	110802749	.	C	T	2958.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=32.098;DP=5000;Dels=0.00;FS=34.851;HaplotypeScore=293.3769;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-32.561;QD=0.59;ReadPosRankSum=-23.064;SOR=6.855	GT:AD:DP:GQ:PL	0/1:4543,450:5000:99:2987,0,93645
13	110813709	.	G	A	30790.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=17.331;DP=3189;Dels=0.00;FS=0.000;HaplotypeScore=125.0348;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=-0.007;QD=9.66;ReadPosRankSum=9.828;SOR=0.696	GT:AD:DP:GQ:PL	0/1:1561,1625:3189:99:30819,0,29191
13	110817171	.	G	C	36886.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-40.523;DP=4050;Dels=0.00;FS=0.000;HaplotypeScore=117.6718;MLEAC=1;MLEAF=0.500;MQ=37.02;MQ0=0;MQRankSum=-1.415;QD=9.11;ReadPosRankSum=-1.080;SOR=0.409	GT:AD:DP:GQ:PL	0/1:2363,1680:4050:99:36915,0,60610
13	110818598	.	T	G	43543.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-59.455;DP=4998;Dels=0.00;FS=0.000;HaplotypeScore=2728.1673;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-0.878;QD=8.71;ReadPosRankSum=-0.191;SOR=0.682	GT:AD:DP:GQ:PL	0/1:2503,2476:4998:99:43572,0,58983
13	110826770	.	T	A	336.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.323;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.441;QD=19.81;ReadPosRankSum=0.063;SOR=2.712	GT:AD:DP:GQ:PL	0/1:3,14:17:40:365,0,40
13	110835317	.	C	CA	5261.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.992;DP=2572;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.59;MQ0=0;MQRankSum=-1.304;QD=2.05;RPA=12,13;RU=A;ReadPosRankSum=1.329;SOR=0.103;STR	GT:AD:DP:GQ:PL	0/1:1868,704:2572:99:5299,0,22737
13	110839550	.	T	G	27727.77	.	AC=2;AF=1.00;AN=2;DP=902;Dels=0.00;FS=0.000;HaplotypeScore=49.3213;MLEAC=2;MLEAF=1.00;MQ=59.74;MQ0=0;QD=30.74;SOR=13.607	GT:AD:DP:GQ:PL	1/1:0,900:901:99:27756,2700,0
13	110844721	.	C	T	73498.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=3.669;DP=2474;Dels=0.00;FS=0.000;HaplotypeScore=174.6027;MLEAC=2;MLEAF=1.00;MQ=59.66;MQ0=0;MQRankSum=0.417;QD=29.71;ReadPosRankSum=2.793;SOR=10.478	GT:AD:DP:GQ:PL	1/1:12,2449:2474:99:73527,6810,0
13	110845314	.	G	A	70527.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=4.314;DP=2638;Dels=0.00;FS=0.000;HaplotypeScore=246.5446;MLEAC=2;MLEAF=1.00;MQ=59.24;MQ0=0;MQRankSum=-2.336;QD=26.74;ReadPosRankSum=0.304;SOR=10.460	GT:AD:DP:GQ:PL	1/1:13,2614:2637:99:70556,7747,0
13	110850770	.	T	C	57564.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-3.934;DP=2640;Dels=0.00;FS=0.000;HaplotypeScore=133.9278;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;MQRankSum=-0.818;QD=21.80;ReadPosRankSum=1.129;SOR=0.694	GT:AD:DP:GQ:PL	1/1:12,2627:2640:99:57593,3714,0
13	110851014	.	G	C	68263.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.722;DP=2896;Dels=0.00;FS=0.000;HaplotypeScore=206.9397;MLEAC=2;MLEAF=1.00;MQ=59.41;MQ0=0;MQRankSum=-0.496;QD=23.57;ReadPosRankSum=1.131;SOR=14.551	GT:AD:DP:GQ:PL	1/1:1,2888:2894:99:68292,8575,0
13	110853391	.	A	C	122.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.633;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.00;MQ0=0;MQRankSum=0.633;QD=12.28;ReadPosRankSum=-0.633;SOR=1.085	GT:AD:DP:GQ:PL	0/1:4,6:10:90:151,0,90
13	110856085	.	A	G	67057.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-2.322;DP=2575;Dels=0.00;FS=0.000;HaplotypeScore=247.3687;MLEAC=2;MLEAF=1.00;MQ=57.61;MQ0=121;MQRankSum=-0.447;QD=26.04;ReadPosRankSum=1.120;SOR=13.413	GT:AD:DP:GQ:PL	1/1:2,2573:2575:99:67086,7143,0
13	110857823	.	C	T	26176.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.282;DP=1189;Dels=0.00;FS=0.000;HaplotypeScore=62.3109;MLEAC=2;MLEAF=1.00;MQ=59.83;MQ0=0;MQRankSum=0.439;QD=22.02;ReadPosRankSum=-0.520;SOR=0.705	GT:AD:DP:GQ:PL	1/1:2,1183:1189:99:26205,1749,0
13	110857895	.	A	G	17537.77	.	AC=2;AF=1.00;AN=2;DP=598;Dels=0.00;FS=0.000;HaplotypeScore=38.5909;MLEAC=2;MLEAF=1.00;MQ=59.70;MQ0=0;QD=29.33;SOR=12.787	GT:AD:DP:GQ:PL	1/1:0,597:598:99:17566,1788,0
13	110859316	.	GA	G	6631.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=12.320;DP=5000;FS=11.976;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-2.530;QD=1.33;RPA=12,11;RU=A;ReadPosRankSum=-2.638;SOR=1.221;STR	GT:AD:DP:GQ:PL	0/1:3910,1083:5000:99:6669,0,75001
13	110859743	.	C	T	99526.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.769;DP=3295;Dels=0.00;FS=0.000;HaplotypeScore=218.1686;MLEAC=2;MLEAF=1.00;MQ=59.78;MQ0=0;MQRankSum=0.897;QD=30.21;ReadPosRankSum=-1.196;SOR=10.644	GT:AD:DP:GQ:PL	1/1:15,3275:3295:99:99555,9433,0
13	110861785	.	C	G	130113.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=2.310;DP=5000;Dels=0.00;FS=0.000;HaplotypeScore=292.6942;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;MQRankSum=0.217;QD=26.02;ReadPosRankSum=-0.103;SOR=0.168	GT:AD:DP:GQ:PL	1/1:2,4987:4998:99:130142,11462,0
13	110862687	.	T	G	155.84	.	AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.97;SOR=3.912	GT:AD:DP:GQ:PL	1/1:0,6:6:18:184,18,0
13	110864225	.	A	T	124659.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.729;DP=5000;Dels=0.00;FS=0.000;HaplotypeScore=289.5051;MLEAC=2;MLEAF=1.00;MQ=59.95;MQ0=0;MQRankSum=0.262;QD=24.93;ReadPosRankSum=0.078;SOR=0.482	GT:AD:DP:GQ:PL	1/1:5,4968:5000:99:124688,10117,0
13	110895092	.	A	G	53170.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-51.519;DP=5000;Dels=0.00;FS=0.000;HaplotypeScore=311.6738;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=0.275;QD=10.63;ReadPosRankSum=-2.537;SOR=0.734	GT:AD:DP:GQ:PL	0/1:2473,2526:5000:99:53199,0,53230
13	110895150	.	A	G	28014.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-36.569;DP=2456;Dels=0.00;FS=0.000;HaplotypeScore=164.3525;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.512;QD=11.41;ReadPosRankSum=0.199;SOR=0.697	GT:AD:DP:GQ:PL	0/1:1224,1229:2456:99:28043,0,29631
13	110959356	.	C	G	29822.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=31.454;DP=1850;Dels=0.00;FS=8.413;HaplotypeScore=112.2341;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=1.280;QD=16.12;ReadPosRankSum=-1.627;SOR=1.222	GT:AD:DP:GQ:PL	0/1:665,1182:1850:99:29851,0,11983
13	110959464	.	C	A	15200.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.082;DP=2610;Dels=0.00;FS=0.000;HaplotypeScore=171.0747;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.235;QD=5.82;ReadPosRankSum=-1.195;SOR=0.685	GT:AD:DP:GQ:PL	0/1:1747,861:2610:99:15229,0,34732
13	111076987	.	C	CA	288.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;DP=65;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-1.221;QD=4.44;RPA=11,12;RU=A;ReadPosRankSum=0.971;SOR=0.258;STR	GT:AD:DP:GQ:PL	0/1:47,18:65:99:326,0,722
13	111077197	.	G	A	115126.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=4.054;DP=5000;Dels=0.00;FS=0.000;HaplotypeScore=281.2811;MLEAC=2;MLEAF=1.00;MQ=59.87;MQ0=0;MQRankSum=-0.852;QD=23.03;ReadPosRankSum=-0.360;SOR=0.698	GT:AD:DP:GQ:PL	1/1:12,4985:5000:99:115155,8145,0
13	111077400	.	AT	A	91690.73	.	AC=2;AF=1.00;AN=2;DP=5000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.65;MQ0=0;QD=18.34;RPA=4,3;RU=T;SOR=1.107;STR	GT:AD:DP:GQ:PL	1/1:0,4994:4995:99:91728,14630,0
13	111077450	.	G	A	88471.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=2.819;DP=2978;Dels=0.00;FS=0.000;HaplotypeScore=159.2950;MLEAC=2;MLEAF=1.00;MQ=59.24;MQ0=0;MQRankSum=-1.340;QD=29.71;ReadPosRankSum=-0.316;SOR=12.776	GT:AD:DP:GQ:PL	1/1:4,2973:2978:99:88500,8812,0
13	111091024	.	C	T	61813.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=58.035;DP=5000;Dels=0.00;FS=0.522;HaplotypeScore=373.1499;MLEAC=1;MLEAF=0.500;MQ=59.95;MQ0=0;MQRankSum=-0.319;QD=12.36;ReadPosRankSum=-2.891;SOR=0.766	GT:AD:DP:GQ:PL	0/1:2381,2614:5000:99:61842,0,46977
13	111098226	.	C	T	57203.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-48.538;DP=4606;Dels=0.00;FS=0.000;HaplotypeScore=264.1278;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=3.150;QD=12.42;ReadPosRankSum=-4.989;SOR=1.753	GT:AD:DP:GQ:PL	0/1:2200,2402:4606:99:57232,0,52332
13	111098338	.	A	T	71962.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.341;DP=2492;Dels=0.00;FS=0.000;HaplotypeScore=245.0166;MLEAC=2;MLEAF=1.00;MQ=59.25;MQ0=0;MQRankSum=0.111;QD=28.88;ReadPosRankSum=1.101;SOR=13.429	GT:AD:DP:GQ:PL	1/1:2,2472:2492:99:71991,6967,0
13	111099122	.	G	A	55226.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-58.869;DP=4887;Dels=0.00;FS=0.000;HaplotypeScore=290.0129;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-0.047;QD=11.30;ReadPosRankSum=-2.103;SOR=0.752	GT:AD:DP:GQ:PL	0/1:2362,2502:4885:99:55255,0,61982
13	111102042	.	G	A	26901.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=37.673;DP=1967;Dels=0.00;FS=0.000;HaplotypeScore=126.4178;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=-0.554;QD=13.68;ReadPosRankSum=-0.853;SOR=0.787	GT:AD:DP:GQ:PL	0/1:939,1027:1967:99:26930,0,16380
13	111102126	.	C	T	25199.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=37.704;DP=1966;Dels=0.00;FS=0.000;HaplotypeScore=116.9287;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=1.018;QD=12.82;ReadPosRankSum=5.946;SOR=0.790	GT:AD:DP:GQ:PL	0/1:935,1026:1965:99:25228,0,15299
13	111102183	.	A	G	24678.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=6.329;DP=1953;Dels=0.00;FS=0.000;HaplotypeScore=72.8096;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=-0.259;QD=12.64;ReadPosRankSum=5.217;SOR=0.794	GT:AD:DP:GQ:PL	0/1:927,1021:1953:99:24707,0,21036
13	111109576	.	G	C	25477.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-11.800;DP=1174;Dels=0.00;FS=0.000;HaplotypeScore=96.9996;MLEAC=2;MLEAF=1.00;MQ=20.90;MQ0=1;MQRankSum=-5.691;QD=21.70;ReadPosRankSum=0.735;SOR=5.679	GT:AD:DP:GQ:PL	1/1:64,1110:1174:99:25506,1688,0
13	111109618	.	G	C	34642.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-6.799;DP=1447;Dels=0.00;FS=0.000;HaplotypeScore=114.2209;MLEAC=2;MLEAF=1.00;MQ=32.18;MQ0=1;MQRankSum=-4.492;QD=23.94;ReadPosRankSum=-1.628;SOR=7.228	GT:AD:DP:GQ:PL	1/1:37,1410:1447:99:34671,3189,0
13	111109859	.	A	G	78953.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-3.409;DP=3587;Dels=0.00;FS=0.000;HaplotypeScore=231.8311;MLEAC=2;MLEAF=1.00;MQ=59.82;MQ0=0;MQRankSum=0.906;QD=22.01;ReadPosRankSum=0.813;SOR=0.695	GT:AD:DP:GQ:PL	1/1:4,3580:3587:99:78982,5341,0
13	111109882	.	A	G	34429.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-50.515;DP=3587;Dels=0.00;FS=0.000;HaplotypeScore=238.1042;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.960;QD=9.60;ReadPosRankSum=-2.839;SOR=0.690	GT:AD:DP:GQ:PL	0/1:1778,1809:3587:99:34458,0,34181
13	111109960	.	T	C	41992.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.728;DP=1792;Dels=0.00;FS=0.000;HaplotypeScore=43.4683;MLEAC=2;MLEAF=1.00;MQ=59.84;MQ0=0;MQRankSum=-0.191;QD=23.43;ReadPosRankSum=1.353;SOR=13.596	GT:AD:DP:GQ:PL	1/1:1,1791:1792:99:42021,5268,0
13	111111023	.	T	C	78489.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.632;DP=2723;Dels=0.00;FS=0.000;HaplotypeScore=184.2767;MLEAC=2;MLEAF=1.00;MQ=59.33;MQ0=0;MQRankSum=0.102;QD=28.82;ReadPosRankSum=-0.859;SOR=11.204	GT:AD:DP:GQ:PL	1/1:9,2709:2723:99:78518,7761,0
13	111111043	.	G	A	83095.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=4.706;DP=2723;Dels=0.00;FS=0.000;HaplotypeScore=161.9158;MLEAC=2;MLEAF=1.00;MQ=59.33;MQ0=0;MQRankSum=0.428;QD=30.52;ReadPosRankSum=-0.896;SOR=11.411	GT:AD:DP:GQ:PL	1/1:8,2703:2723:99:83124,7809,0
13	111111173	.	G	A	71480.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=3.143;DP=2509;Dels=0.00;FS=0.000;HaplotypeScore=174.2822;MLEAC=2;MLEAF=1.00;MQ=68.79;MQ0=0;MQRankSum=1.934;QD=28.49;ReadPosRankSum=-0.788;SOR=11.037	GT:AD:DP:GQ:PL	1/1:9,2492:2509:99:71509,7114,0
13	111111235	.	G	A	97041.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=3.684;DP=4401;Dels=0.00;FS=0.000;HaplotypeScore=170.7152;MLEAC=2;MLEAF=1.00;MQ=59.95;MQ0=0;MQRankSum=-0.137;QD=22.05;ReadPosRankSum=0.845;SOR=0.695	GT:AD:DP:GQ:PL	1/1:6,4389:4398:99:97070,6498,0
13	111114554	.	G	A	38798.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=39.962;DP=3878;Dels=0.00;FS=0.000;HaplotypeScore=254.0843;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=-1.755;QD=10.00;ReadPosRankSum=4.070;SOR=0.688	GT:AD:DP:GQ:PL	0/1:1860,2015:3877:99:38827,0,34114
13	111114751	.	G	A	19671.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=31.728;DP=2195;Dels=0.00;FS=0.000;HaplotypeScore=106.3253;MLEAC=1;MLEAF=0.500;MQ=59.95;MQ0=0;MQRankSum=0.017;QD=8.96;ReadPosRankSum=2.928;SOR=0.691	GT:AD:DP:GQ:PL	0/1:1163,1032:2195:99:19700,0,22310
13	111117668	.	G	A	22736.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=37.024;DP=1991;Dels=0.00;FS=0.000;HaplotypeScore=119.9721;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=1.074;QD=11.42;ReadPosRankSum=0.088;SOR=0.572	GT:AD:DP:GQ:PL	0/1:1058,929:1990:99:22765,0,18218
13	111117745	.	C	T	87388.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-2.211;DP=3971;Dels=0.00;FS=0.000;HaplotypeScore=277.5134;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;MQRankSum=0.006;QD=22.01;ReadPosRankSum=0.318;SOR=0.554	GT:AD:DP:GQ:PL	1/1:11,3941:3956:99:87417,5717,0
13	111118102	.	G	A	80219.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.387;DP=2795;Dels=0.00;FS=0.000;HaplotypeScore=293.9784;MLEAC=2;MLEAF=1.00;MQ=59.12;MQ0=0;MQRankSum=0.006;QD=28.70;ReadPosRankSum=0.337;SOR=11.067	GT:AD:DP:GQ:PL	1/1:11,2782:2795:99:80248,7988,0
13	111121620	.	C	T	54788.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.626;DP=5000;Dels=0.00;FS=0.515;HaplotypeScore=247.0159;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=-1.043;QD=10.96;ReadPosRankSum=2.453;SOR=0.655	GT:AD:DP:GQ:PL	0/1:2483,2501:4996:99:54817,0,53816
13	111121717	.	A	G	75193.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.737;DP=2555;Dels=0.00;FS=0.000;HaplotypeScore=58.7577;MLEAC=2;MLEAF=1.00;MQ=59.97;MQ0=0;MQRankSum=-0.793;QD=29.43;ReadPosRankSum=-1.762;SOR=13.490	GT:AD:DP:GQ:PL	1/1:2,2549:2555:99:75222,7386,0
13	111121718	.	A	G	62.28	.	AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.76;SOR=2.833	GT:AD:DP:GQ:PL	1/1:0,3:3:9:90,9,0
13	111125606	.	A	G	52289.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=31.110;DP=5000;Dels=0.00;FS=0.000;HaplotypeScore=309.7044;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=0.401;QD=10.46;ReadPosRankSum=-2.615;SOR=0.681	GT:AD:DP:GQ:PL	0/1:2462,2530:4997:99:52318,0,49516
13	111130226	.	G	A	13545.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.336;DP=1235;Dels=0.00;FS=0.000;HaplotypeScore=56.6569;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=-0.232;QD=10.97;ReadPosRankSum=-0.382;SOR=0.566	GT:AD:DP:GQ:PL	0/1:657,573:1235:99:13574,0,16014
13	111130599	.	G	C	7855.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.938;DP=671;Dels=0.00;FS=0.000;HaplotypeScore=14.8964;MLEAC=1;MLEAF=0.500;MQ=59.97;MQ0=0;MQRankSum=0.403;QD=11.71;ReadPosRankSum=0.072;SOR=0.641	GT:AD:DP:GQ:PL	0/1:343,325:671:99:7884,0,8251
13	111132490	.	A	G	33856.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-50.670;DP=3833;Dels=0.00;FS=0.000;HaplotypeScore=314.3893;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=2.383;QD=8.83;ReadPosRankSum=-0.284;SOR=1.622	GT:AD:DP:GQ:PL	0/1:1907,1916:3832:99:33885,0,46742
13	111134858	.	T	C	46147.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-39.138;DP=5000;Dels=0.00;FS=0.000;HaplotypeScore=324.2000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=1;MQRankSum=-0.429;QD=9.23;ReadPosRankSum=-3.969;SOR=0.678	GT:AD:DP:GQ:PL	0/1:2517,2480:5000:99:46176,0,53365
13	111137215	.	A	G	61.28	.	AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=20.43;SOR=2.833	GT:AD:DP:GQ:PL	1/1:0,3:3:9:89,9,0
13	111138255	.	G	A	28829.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=11.072;DP=2480;Dels=0.00;FS=0.000;HaplotypeScore=196.8147;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=-0.262;QD=11.62;ReadPosRankSum=0.157;SOR=0.680	GT:AD:DP:GQ:PL	0/1:1245,1229:2480:99:28858,0,28776
13	111142009	.	A	C	24844.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-44.368;DP=2787;Dels=0.00;FS=0.000;HaplotypeScore=205.5293;MLEAC=1;MLEAF=0.500;MQ=36.91;MQ0=0;MQRankSum=-1.875;QD=8.91;ReadPosRankSum=-0.691;SOR=0.716	GT:AD:DP:GQ:PL	0/1:1374,1405:2787:99:24873,0,32187
13	111142016	.	G	A	34356.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=43.750;DP=2787;Dels=0.00;FS=0.000;HaplotypeScore=175.1071;MLEAC=1;MLEAF=0.500;MQ=36.91;MQ0=0;MQRankSum=-0.338;QD=12.33;ReadPosRankSum=1.281;SOR=0.713	GT:AD:DP:GQ:PL	0/1:1380,1407:2787:99:34385,0,30884
13	111143755	.	T	C	49872.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=2.092;DP=1633;Dels=0.00;FS=0.000;HaplotypeScore=87.2162;MLEAC=2;MLEAF=1.00;MQ=36.97;MQ0=0;MQRankSum=-0.318;QD=30.54;ReadPosRankSum=0.463;SOR=12.015	GT:AD:DP:GQ:PL	1/1:3,1625:1630:99:49901,4793,0
13	111144412	.	C	G	17787.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-37.424;DP=1983;Dels=0.00;FS=0.000;HaplotypeScore=155.7495;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.876;QD=8.97;ReadPosRankSum=0.464;SOR=0.711	GT:AD:DP:GQ:PL	0/1:981,999:1983:99:17816,0,22772
13	111144565	.	C	T	22734.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=35.248;DP=1983;Dels=0.00;FS=0.000;HaplotypeScore=158.5464;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.231;QD=11.46;ReadPosRankSum=7.929;SOR=0.710	GT:AD:DP:GQ:PL	0/1:982,999:1983:99:22763,0,16683
13	111145633	.	C	T	60566.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=40.448;DP=4999;Dels=0.00;FS=0.519;HaplotypeScore=280.9414;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-1.865;QD=12.12;ReadPosRankSum=8.468;SOR=0.647	GT:AD:DP:GQ:PL	0/1:2314,2679:4999:99:60595,0,49030
13	111145676	.	G	C	43209.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-53.537;DP=4999;Dels=0.00;FS=0.519;HaplotypeScore=296.0015;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.223;QD=8.64;ReadPosRankSum=-2.982;SOR=0.745	GT:AD:DP:GQ:PL	0/1:2682,2306:4999:99:43238,0,58391
13	111153985	.	G	A	33.74	.	AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=16.87;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:61,6,0
13	111154058	.	T	A	148071.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=4.083;DP=4788;Dels=0.00;FS=0.000;HaplotypeScore=285.0189;MLEAC=2;MLEAF=1.00;MQ=59.89;MQ0=0;MQRankSum=-0.504;QD=30.93;ReadPosRankSum=-1.359;SOR=13.045	GT:AD:DP:GQ:PL	1/1:6,4762:4786:99:148100,14013,0
13	111154061	.	T	C	140272.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=2.166;DP=4788;Dels=0.00;FS=0.000;HaplotypeScore=279.1178;MLEAC=2;MLEAF=1.00;MQ=59.89;MQ0=0;MQRankSum=0.535;QD=29.30;ReadPosRankSum=-0.972;SOR=12.550	GT:AD:DP:GQ:PL	1/1:8,4779:4788:99:140301,14046,0
13	111154159	.	C	T	29275.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-37.910;DP=2475;Dels=0.00;FS=0.000;HaplotypeScore=171.3361;MLEAC=1;MLEAF=0.500;MQ=59.81;MQ0=0;MQRankSum=-2.080;QD=11.83;ReadPosRankSum=2.335;SOR=0.612	GT:AD:DP:GQ:PL	0/1:1289,1184:2475:99:29304,0,33993
13	111154160	.	G	A	32469.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=40.595;DP=2475;Dels=0.00;FS=0.000;HaplotypeScore=169.7505;MLEAC=1;MLEAF=0.500;MQ=59.81;MQ0=0;MQRankSum=-1.613;QD=13.12;ReadPosRankSum=1.810;SOR=0.764	GT:AD:DP:GQ:PL	0/1:1194,1279:2475:99:32498,0,27433
13	111155363	.	G	A	152817.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=4.554;DP=5000;Dels=0.00;FS=0.000;HaplotypeScore=279.4230;MLEAC=2;MLEAF=1.00;MQ=59.72;MQ0=0;MQRankSum=-0.460;QD=30.56;ReadPosRankSum=0.570;SOR=11.747	GT:AD:DP:GQ:PL	1/1:13,4976:4998:99:152846,14408,0
13	111155428	.	C	T	128957.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.409;DP=5000;Dels=0.00;FS=0.000;HaplotypeScore=275.8911;MLEAC=2;MLEAF=1.00;MQ=59.82;MQ0=0;MQRankSum=2.163;QD=25.79;ReadPosRankSum=0.947;SOR=0.436	GT:AD:DP:GQ:PL	1/1:15,4979:4999:99:128986,10910,0
13	111155711	.	C	T	21314.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=32.688;DP=1696;Dels=0.00;FS=0.000;HaplotypeScore=128.9425;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=0.032;QD=12.57;ReadPosRankSum=-0.907;SOR=0.744	GT:AD:DP:GQ:PL	0/1:825,867:1696:99:21343,0,18557
13	111155773	.	T	C	74161.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.351;DP=3378;Dels=0.00;FS=0.000;HaplotypeScore=175.7761;MLEAC=2;MLEAF=1.00;MQ=59.88;MQ0=0;MQRankSum=0.695;QD=21.95;ReadPosRankSum=-0.079;SOR=0.695	GT:AD:DP:GQ:PL	1/1:8,3359:3372:99:74190,4911,0
13	111155779	.	G	A	33044.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=12.744;DP=3378;Dels=0.00;FS=0.000;HaplotypeScore=148.2723;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=-0.610;QD=9.78;ReadPosRankSum=-0.109;SOR=0.698	GT:AD:DP:GQ:PL	0/1:1655,1719:3378:99:33073,0,31340
13	111156153	.	G	A	50283.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=57.418;DP=5000;Dels=0.00;FS=0.000;HaplotypeScore=307.5635;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=0.341;QD=10.06;ReadPosRankSum=4.758;SOR=0.669	GT:AD:DP:GQ:PL	0/1:2526,2470:5000:99:50312,0,48881
13	111156411	.	G	A	49505.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=17.515;DP=5000;Dels=0.00;FS=0.516;HaplotypeScore=284.8518;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=1.690;QD=9.90;ReadPosRankSum=2.157;SOR=0.711	GT:AD:DP:GQ:PL	0/1:2491,2473:5000:99:49534,0,43338
13	111156499	.	C	T	77892.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-0.395;DP=2643;Dels=0.00;FS=0.000;HaplotypeScore=165.7065;MLEAC=2;MLEAF=1.00;MQ=59.74;MQ0=0;MQRankSum=0.196;QD=29.47;ReadPosRankSum=0.746;SOR=11.147	GT:AD:DP:GQ:PL	1/1:9,2633:2643:99:77921,7487,0
13	111158567	.	A	T	189.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.752;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=2.9874;MLEAC=1;MLEAF=0.500;MQ=29.67;MQ0=1;MQRankSum=-1.270;QD=9.99;ReadPosRankSum=-0.423;SOR=0.941	GT:AD:DP:GQ:PL	0/1:8,9:19:99:218,0,164
13	111158579	.	G	A	805.90	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.343;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=3.8387;MLEAC=1;MLEAF=0.500;MQ=29.06;MQ0=1;MQRankSum=-1.021;QD=20.66;ReadPosRankSum=-1.861;SOR=3.145	GT:AD:DP:GQ:PL	0/1:7,32:39:15:834,0,15
13	111158585	.	C	T	776.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=7.7259;MLEAC=1;MLEAF=0.500;MQ=29.06;MQ0=1;MQRankSum=-0.640;QD=19.92;ReadPosRankSum=-1.883;SOR=2.833	GT:AD:DP:GQ:PL	0/1:8,31:39:40:805,0,40
13	111158590	.	A	G	896.89	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.541;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=17.4756;MLEAC=1;MLEAF=0.500;MQ=29.06;MQ0=1;MQRankSum=-2.677;QD=23.00;ReadPosRankSum=-3.152;SOR=3.500	GT:AD:DP:GQ:PL	0/1:6,33:39:2:923,0,2
13	111158604	.	ACTCTCTCT	A,ACTCTCT	3134.73	.	AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=3.967;DP=104;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=33.17;MQ0=0;MQRankSum=-4.033;QD=18.08;RPA=11,7,10;RU=CT;ReadPosRankSum=2.799;SOR=0.663;STR	GT:AD:DP:GQ:PL	1/2:32,38,31:101:99:3172,194,3786,1713,0,2247
13	111158614	.	T	C	497.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.720;DP=108;Dels=0.02;FS=0.000;HaplotypeScore=420.8422;MLEAC=1;MLEAF=0.500;MQ=33.03;MQ0=1;MQRankSum=4.330;QD=4.61;ReadPosRankSum=-5.224;SOR=0.154	GT:AD:DP:GQ:PL	0/1:75,31:106:99:526,0,1837
13	111158623	.	C	T	564.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=7.042;DP=113;Dels=0.01;FS=0.000;HaplotypeScore=66.5141;MLEAC=1;MLEAF=0.500;MQ=32.86;MQ0=1;MQRankSum=-6.081;QD=5.00;ReadPosRankSum=7.313;SOR=0.170	GT:AD:DP:GQ:PL	0/1:79,33:112:99:593,0,1896
13	111158874	.	A	G	13963.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.721;DP=1470;Dels=0.00;FS=0.000;HaplotypeScore=77.6106;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=0.779;QD=9.50;ReadPosRankSum=0.761;SOR=0.707	GT:AD:DP:GQ:PL	0/1:733,736:1470:99:13992,0,13995
13	111164198	.	T	C	19059.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-32.675;DP=1783;Dels=0.00;FS=0.000;HaplotypeScore=160.2593;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=1.595;QD=10.69;ReadPosRankSum=0.779;SOR=0.608	GT:AD:DP:GQ:PL	0/1:931,852:1783:99:19088,0,23156
13	111164614	.	T	C	47057.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-13.273;DP=5000;Dels=0.00;FS=4.100;HaplotypeScore=413.5352;MLEAC=1;MLEAF=0.500;MQ=59.24;MQ0=0;MQRankSum=1.356;QD=9.41;ReadPosRankSum=-20.215;SOR=1.083	GT:AD:DP:GQ:PL	0/1:2670,2315:4999:99:47086,0,54067
13	111164628	.	TAA	T	19111.73	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-0.073;DP=2491;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.43;MQ0=0;MQRankSum=1.112;QD=7.67;RPA=12,10;RU=A;ReadPosRankSum=-32.661;SOR=0.788;STR	GT:AD:DP:GQ:PL	0/1:1452,1029:2481:99:19149,0,27348