##fileformat=VCFv4.1 ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[realigned_ind15.rmdup.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=../16/Ind16-final1.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=8000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null defaultBaseQualities=-1 validation_strictness=SILENT 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 logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.05 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 noSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=1.0 max_alternate_alleles=20 min_indel_count_for_genotyping=5 indel_heterozygosity=0.05 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 noBandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false" ##contig= ##reference=file:///data/home/amanda.brown/Amanda1/Ishi/GATK/16-15/../16/Ind16-final1.fa #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 16_15 Ind16 32073 . GA G 35.53 . AC=1;AF=0.50;AN=2;BaseQRankSum=4.460;DP=150;FS=0.000;HRun=6;HaplotypeScore=226.5186;MQ=26.53;MQ0=41;MQRankSum=-0.831;QD=0.24;ReadPosRankSum=-0.565;SB=-15.70 GT:AD:DP:GQ:PL 0/1:139,11:96:48.20:48,0,2908 Ind16 33107 . C CAA 4317.11 . AC=2;AF=1.00;AN=2;DP=82;FS=0.000;HRun=0;HaplotypeScore=162.2901;MQ=46.89;MQ0=6;QD=52.65;SB=-1767.05 GT:AD:DP:GQ:PL 1/1:3,76:73:99:4317,217,0 Ind16 36984 . T C 6906.94 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.708;DP=186;Dels=0.00;FS=3.783;HRun=0;HaplotypeScore=3.8993;MQ=52.06;MQ0=0;MQRankSum=0.000;QD=37.13;ReadPosRankSum=0.726;SB=-3026.50 GT:AD:DP:GQ:PL 1/1:1,185:186:99:6907,511,0 Ind16 260208 . T G 1338.45 . AC=1;AF=0.50;AN=2;BaseQRankSum=-0.293;DP=163;Dels=0.00;FS=0.859;HRun=0;HaplotypeScore=0.0000;MQ=36.43;MQ0=42;MQRankSum=2.129;QD=8.21;ReadPosRankSum=0.075;SB=-556.30 GT:AD:DP:GQ:PL 0/1:82,81:163:99:1351,0,1044 Ind16 260209 . C A 1230.48 . AC=1;AF=0.50;AN=2;BaseQRankSum=-2.505;DP=166;Dels=0.00;FS=5.685;HRun=0;HaplotypeScore=0.0000;MQ=35.88;MQ0=43;MQRankSum=1.686;QD=7.41;ReadPosRankSum=0.918;SB=-468.33 GT:AD:DP:GQ:PL 0/1:89,77:166:99:1243,0,1201 Ind16 260271 . T G 518.71 . AC=1;AF=0.50;AN=2;BaseQRankSum=1.518;DP=152;Dels=0.00;FS=2.597;HRun=0;HaplotypeScore=0.0000;MQ=26.69;MQ0=50;MQRankSum=0.141;QD=3.41;ReadPosRankSum=-2.896;SB=-225.60 GT:AD:DP:GQ:PL 0/1:97,55:152:99:531,0,878 Ind16 260272 . C A 479.39 . AC=1;AF=0.50;AN=2;BaseQRankSum=-1.672;DP=150;Dels=0.00;FS=2.704;HRun=0;HaplotypeScore=0.0000;MQ=26.46;MQ0=50;MQRankSum=0.479;QD=3.20;ReadPosRankSum=-2.539;SB=-195.45 GT:AD:DP:GQ:PL 0/1:97,53:150:99:492,0,886 Ind16 260481 . G T 580.39 . AC=1;AF=0.50;AN=2;BaseQRankSum=-3.295;DP=101;Dels=0.00;FS=10.328;HRun=0;HaplotypeScore=0.0000;MQ=29.86;MQ0=23;MQRankSum=-0.211;QD=5.75;ReadPosRankSum=-2.371;SB=-87.24 GT:AD:DP:GQ:PL 0/1:58,43:101:99:593,0,557 Ind16 260482 . A C 618.55 . AC=1;AF=0.50;AN=2;BaseQRankSum=-1.040;DP=103;Dels=0.00;FS=9.720;HRun=1;HaplotypeScore=0.0000;MQ=30.73;MQ0=23;MQRankSum=-0.150;QD=6.01;ReadPosRankSum=-2.103;SB=-121.22 GT:AD:DP:GQ:PL 0/1:59,44:103:99:631,0,585 Ind16 300647 . C T 3192.49 . AC=1;AF=0.50;AN=2;BaseQRankSum=-0.593;DP=218;Dels=0.00;FS=355.283;HRun=0;HaplotypeScore=5.7874;MQ=26.73;MQ0=0;MQRankSum=12.022;QD=14.64;ReadPosRankSum=-0.326;SB=-409.41 GT:AD:DP:GQ:PL 0/1:102,116:218:99:3205,0,2194 Ind16 301430 . G A 4448.15 . AC=2;AF=1.00;AN=2;DP=163;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=28.37;MQ0=19;QD=27.29;SB=-2169.27 GT:AD:DP:GQ:PL 1/1:13,150:163:99:4448,382,0 Ind16 301434 . A T 4650.14 . AC=2;AF=1.00;AN=2;DP=168;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=28.66;MQ0=19;QD=27.68;SB=-2247.47 GT:AD:DP:GQ:PL 1/1:13,155:168:99:4650,400,0 Ind16 318605 . A T 53.02 . AC=1;AF=0.50;AN=2;BaseQRankSum=-1.752;DP=150;Dels=0.00;FS=12.030;HRun=1;HaplotypeScore=14.9960;MQ=46.20;MQ0=1;MQRankSum=-3.952;QD=0.35;ReadPosRankSum=-5.028;SB=-0.34 GT:AD:DP:GQ:PL 0/1:137,13:150:65.69:66,0,4902 Ind16 318607 . A T 59.18 . AC=1;AF=0.50;AN=2;BaseQRankSum=0.352;DP=149;Dels=0.00;FS=9.620;HRun=1;HaplotypeScore=14.9960;MQ=45.60;MQ0=1;MQRankSum=-2.737;QD=0.40;ReadPosRankSum=-4.579;SB=-0.34 GT:AD:DP:GQ:PL 0/1:136,13:149:71.85:72,0,4833 Ind16 318614 . A G 189.50 . AC=1;AF=0.50;AN=2;BaseQRankSum=-0.707;DP=157;Dels=0.00;FS=8.097;HRun=0;HaplotypeScore=5.9984;MQ=44.63;MQ0=2;MQRankSum=-3.851;QD=1.21;ReadPosRankSum=-3.644;SB=-0.34 GT:AD:DP:GQ:PL 0/1:137,20:157:99:202,0,4942 Ind16 318621 . A G 734.51 . AC=1;AF=0.50;AN=2;BaseQRankSum=-0.365;DP=178;Dels=0.00;FS=12.491;HRun=0;HaplotypeScore=0.9997;MQ=44.23;MQ0=2;MQRankSum=-4.356;QD=4.13;ReadPosRankSum=-4.279;SB=-29.99 GT:AD:DP:GQ:PL 0/1:144,33:178:99:747,0,5059 Ind16 605829 . A G 2715.13 . AC=1;AF=0.50;AN=2;BaseQRankSum=0.465;DP=222;Dels=0.00;FS=374.014;HRun=1;HaplotypeScore=18.3852;MQ=25.83;MQ0=4;MQRankSum=12.236;QD=12.23;ReadPosRankSum=-0.961;SB=-242.10 GT:AD:DP:GQ:PL 0/1:115,106:221:99:2728,0,2537 Ind16 697711 . TA T 1887.99 . AC=2;AF=1.00;AN=2;DP=93;FS=0.000;HRun=4;HaplotypeScore=169.9235;MQ=35.16;MQ0=17;QD=20.30;SB=-431.86 GT:AD:DP:GQ:PL 1/1:8,85:61:99:1904,159,0 Ind16 698062 . TA T 308.05 . AC=2;AF=1.00;AN=2;DP=41;FS=0.000;HRun=4;HaplotypeScore=21.7184;MQ=13.74;MQ0=30;QD=7.51 GT:AD:DP:GQ:PL 1/1:4,37:9:27.08:324,27,0 Ind16 698764 . TA T 1887.09 . AC=2;AF=1.00;AN=2;DP=100;FS=0.000;HRun=4;HaplotypeScore=136.0087;MQ=16.46;MQ0=35;QD=18.87 GT:AD:DP:GQ:PL 1/1:7,93:53:99:1903,159,0 Ind16 698875 . T C 48.40 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.885;DP=45;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=4.4656;MQ=9.40;MQ0=13;MQRankSum=1.766;QD=1.08;ReadPosRankSum=-0.734 GT:AD:DP:GQ:PL 1/1:24,20:45:5.99:62,6,0 Ind16 698992 . T C 1629.72 . AC=1;AF=0.50;AN=2;BaseQRankSum=1.985;DP=321;Dels=0.00;FS=5.250;HRun=0;HaplotypeScore=4.5711;MQ=42.79;MQ0=7;MQRankSum=-8.531;QD=5.08;ReadPosRankSum=3.043;SB=-1197.36 GT:AD:DP:GQ:PL 0/1:183,138:321:99:1642,0,4749 Ind16 744362 . G A 488.29 . AC=1;AF=0.50;AN=2;BaseQRankSum=-0.410;DP=316;Dels=0.00;FS=102.447;HRun=0;HaplotypeScore=0.9997;MQ=24.16;MQ0=132;MQRankSum=-4.907;QD=1.55;ReadPosRankSum=-1.594;SB=-0.34 GT:AD:DP:GQ:PL 0/1:284,31:316:99:501,0,4728 Ind16 744799 . T C 872.67 . AC=1;AF=0.50;AN=2;BaseQRankSum=-0.869;DP=287;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.9983;MQ=21.49;MQ0=157;MQRankSum=-6.086;QD=3.04;ReadPosRankSum=-0.813 GT:AD:DP:GQ:PL 0/1:248,39:287:99:885,0,2918