##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_ind11.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/16-11/../16/Ind16-final1.fa #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 16_11 Ind16 33107 . C CAA 2039.16 . AC=2;AF=1.00;AN=2;DP=70;FS=0.000;HRun=0;HaplotypeScore=121.8637;MQ=35.37;MQ0=29;QD=29.13;SB=-395.41 GT:AD:DP:GQ:PL 1/1:2,61:38:99:2055,111,0 Ind16 33108 . C A 31.40 . AC=1;AF=0.50;AN=2;BaseQRankSum=-2.232;DP=70;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=35.37;MQ0=29;MQRankSum=2.141;QD=0.45;ReadPosRankSum=-3.269;SB=-14.53 GT:AD:DP:GQ:PL 0/1:65,4:69:44.07:44,0,1139 Ind16 36984 . T C 5983.13 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.963;DP=162;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.9995;MQ=59.13;MQ0=0;MQRankSum=-1.464;QD=36.93;ReadPosRankSum=1.342;SB=-1829.23 GT:AD:DP:GQ:PL 1/1:2,160:162:99:5983,370,0 Ind16 166560 . A C 421.88 . AC=1;AF=0.50;AN=2;BaseQRankSum=1.466;DP=106;Dels=0.00;FS=8.999;HRun=0;HaplotypeScore=8.7231;MQ=59.78;MQ0=0;MQRankSum=0.873;QD=3.98;ReadPosRankSum=-0.807;SB=-120.38 GT:AD:DP:GQ:PL 0/1:87,19:106:99:435,0,2886 Ind16 260208 . T G 1076.55 . AC=1;AF=0.50;AN=2;BaseQRankSum=1.171;DP=179;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=4.8990;MQ=37.30;MQ0=41;MQRankSum=1.547;QD=6.01;ReadPosRankSum=-0.181;SB=-666.05 GT:AD:DP:GQ:PL 0/1:111,68:179:99:1089,0,1747 Ind16 260209 . C A 1067.47 . AC=1;AF=0.50;AN=2;BaseQRankSum=-1.377;DP=183;Dels=0.00;FS=0.723;HRun=0;HaplotypeScore=4.8990;MQ=37.66;MQ0=41;MQRankSum=1.066;QD=5.83;ReadPosRankSum=-0.015;SB=-610.42 GT:AD:DP:GQ:PL 0/1:115,67:183:99:1080,0,1898 Ind16 260271 . T G 482.75 . AC=1;AF=0.50;AN=2;BaseQRankSum=-1.660;DP=151;Dels=0.00;FS=8.433;HRun=0;HaplotypeScore=0.9998;MQ=32.48;MQ0=47;MQRankSum=-0.070;QD=3.20;ReadPosRankSum=-4.665;SB=-225.78 GT:AD:DP:GQ:PL 0/1:109,42:151:99:495,0,1433 Ind16 260272 . C A 411.27 . AC=1;AF=0.50;AN=2;BaseQRankSum=-1.412;DP=148;Dels=0.00;FS=9.309;HRun=0;HaplotypeScore=0.9998;MQ=32.68;MQ0=47;MQRankSum=0.075;QD=2.78;ReadPosRankSum=-4.064;SB=-186.31 GT:AD:DP:GQ:PL 0/1:109,39:148:99:424,0,1442 Ind16 260481 . G T 586.22 . AC=1;AF=0.50;AN=2;BaseQRankSum=-2.578;DP=75;Dels=0.00;FS=4.257;HRun=0;HaplotypeScore=0.9997;MQ=40.40;MQ0=18;MQRankSum=2.139;QD=7.82;ReadPosRankSum=-3.961;SB=-187.80 GT:AD:DP:GQ:PL 0/1:47,28:75:99:599,0,791 Ind16 260482 . A C 583.36 . AC=1;AF=0.50;AN=2;BaseQRankSum=0.472;DP=72;Dels=0.00;FS=2.729;HRun=1;HaplotypeScore=0.0000;MQ=40.85;MQ0=18;MQRankSum=1.609;QD=8.10;ReadPosRankSum=-4.058;SB=-193.52 GT:AD:DP:GQ:PL 0/1:44,28:72:99:596,0,745 Ind16 260502 . G T 96.16 . AC=1;AF=0.50;AN=2;BaseQRankSum=0.207;DP=58;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.9999;MQ=47.51;MQ0=11;MQRankSum=1.100;QD=1.66;ReadPosRankSum=-1.833;SB=-36.64 GT:AD:DP:GQ:PL 0/1:48,10:58:99:109,0,1370 Ind16 260503 . A C 94.78 . AC=1;AF=0.50;AN=2;BaseQRankSum=0.733;DP=59;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.9999;MQ=47.75;MQ0=11;MQRankSum=-0.546;QD=1.61;ReadPosRankSum=-1.793;SB=-33.64 GT:AD:DP:GQ:PL 0/1:49,10:59:99:107,0,1372 Ind16 280413 . TG T 574.25 . AC=1;AF=0.50;AN=2;BaseQRankSum=3.702;DP=158;FS=2.338;HRun=1;HaplotypeScore=474.4204;MQ=59.14;MQ0=0;MQRankSum=0.127;QD=3.63;ReadPosRankSum=-1.261;SB=-0.34 GT:AD:DP:GQ:PL 0/1:153,5:158:99:587,0,6713 Ind16 300647 . C T 1480.59 . AC=1;AF=0.50;AN=2;BaseQRankSum=-0.986;DP=229;Dels=0.00;FS=345.024;HRun=0;HaplotypeScore=0.9933;MQ=28.79;MQ0=6;MQRankSum=6.680;QD=6.47;ReadPosRankSum=-1.288;SB=-0.34 GT:AD:DP:GQ:PL 0/1:160,69:229:99:1493,0,3619 Ind16 301430 . G A 2143.47 . AC=2;AF=1.00;AN=2;DP=115;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=23.14;MQ0=42;QD=18.64;SB=-591.00 GT:AD:DP:GQ:PL 1/1:29,85:115:99:2159,189,0 Ind16 301434 . A T 2160.90 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.409;DP=119;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=7.9457;MQ=22.97;MQ0=44;MQRankSum=0.670;QD=18.16;ReadPosRankSum=1.640;SB=-617.68 GT:AD:DP:GQ:PL 1/1:29,90:119:99:2177,165,0 Ind16 318614 . A G 289.37 . AC=1;AF=0.50;AN=2;BaseQRankSum=-4.379;DP=148;Dels=0.00;FS=24.070;HRun=0;HaplotypeScore=2.9992;MQ=47.14;MQ0=0;MQRankSum=-3.004;QD=1.96;ReadPosRankSum=-5.102;SB=-0.34 GT:AD:DP:GQ:PL 0/1:129,19:148:99:302,0,4448 Ind16 318621 . A G 583.88 . AC=1;AF=0.50;AN=2;BaseQRankSum=-4.140;DP=159;Dels=0.00;FS=15.070;HRun=0;HaplotypeScore=7.8982;MQ=46.66;MQ0=0;MQRankSum=-3.902;QD=3.67;ReadPosRankSum=-5.457;SB=-240.49 GT:AD:DP:GQ:PL 0/1:132,27:159:99:597,0,4536 Ind16 367431 . T TAGAG 538.11 . AC=1;AF=0.50;AN=2;BaseQRankSum=3.781;DP=170;FS=14.760;HRun=0;HaplotypeScore=720.5301;MQ=59.37;MQ0=0;MQRankSum=0.186;QD=3.17;ReadPosRankSum=-2.789;SB=-0.34 GT:AD:DP:GQ:PL 0/1:159,11:170:99:551,0,9199 Ind16 605829 . A G 1694.58 . AC=1;AF=0.50;AN=2;BaseQRankSum=-0.621;DP=224;Dels=0.00;FS=334.520;HRun=1;HaplotypeScore=0.0000;MQ=30.35;MQ0=8;MQRankSum=4.752;QD=7.57;ReadPosRankSum=-2.823;SB=-0.34 GT:AD:DP:GQ:PL 0/1:147,77:224:99:1707,0,3285 Ind16 697711 . TA T 1171.23 . AC=2;AF=1.00;AN=2;DP=47;FS=0.000;HRun=4;HaplotypeScore=82.1973;MQ=39.13;MQ0=13;QD=24.92;SB=-180.15 GT:AD:DP:GQ:PL 1/1:2,45:34:99:1187,99,0 Ind16 697822 . T C 280.53 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=15.98;MQ0=6;QD=14.76 GT:AD:DP:GQ:PL 1/1:5,14:19:35.95:296,36,0 Ind16 697828 . TA T 415.94 . AC=2;AF=1.00;AN=2;DP=15;FS=0.000;HRun=4;HaplotypeScore=76.0785;MQ=17.89;MQ0=3;QD=27.73 GT:AD:DP:GQ:PL 1/1:1,14:12:36.11:432,36,0 Ind16 698764 . TA T 1074.89 . AC=2;AF=1.00;AN=2;DP=61;FS=0.000;HRun=4;HaplotypeScore=140.9835;MQ=16.90;MQ0=12;QD=17.62 GT:AD:DP:GQ:PL 1/1:4,57:24:69.21:1091,69,0 Ind16 698992 . T C 972.30 . AC=1;AF=0.50;AN=2;BaseQRankSum=0.771;DP=181;Dels=0.00;FS=7.280;HRun=0;HaplotypeScore=0.9789;MQ=38.72;MQ0=1;MQRankSum=-7.689;QD=5.37;ReadPosRankSum=1.386;SB=-504.63 GT:AD:DP:GQ:PL 0/1:100,81:181:99:985,0,2732 Ind16 744362 . G A 226.39 . AC=1;AF=0.50;AN=2;BaseQRankSum=2.015;DP=251;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.9578;MQ=16.36;MQ0=185;MQRankSum=-2.628;QD=0.90;ReadPosRankSum=0.081 GT:AD:DP:GQ:PL 0/1:237,13:251:99:239,0,1695