Last active
March 7, 2016 13:16
-
-
Save bunop/2ced1915e55e74348e62 to your computer and use it in GitHub Desktop.
htslib can't deal with positions above ~500000000 - resolved - see comments
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ##fileformat=VCFv4.1 | |
| ##fileDate=20150619 | |
| ##source=freeBayes v0.9.20 | |
| ##phasing=none | |
| ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> | |
| ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> | |
| ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> | |
| ##INFO=<ID=AC,Number=.,Type=Integer,Description="Total number of alternate alleles in called genotypes"> | |
| ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | |
| ##INFO=<ID=AF,Number=.,Type=Float,Description="Estimated allele frequency in the range (0,1]"> | |
| ##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> | |
| ##INFO=<ID=AO,Number=.,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> | |
| ##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> | |
| ##INFO=<ID=PAO,Number=.,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> | |
| ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> | |
| ##INFO=<ID=QA,Number=.,Type=Integer,Description="Alternate allele quality sum in phred"> | |
| ##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> | |
| ##INFO=<ID=PQA,Number=.,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> | |
| ##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> | |
| ##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> | |
| ##INFO=<ID=SAF,Number=.,Type=Integer,Description="Number of alternate observations on the forward strand"> | |
| ##INFO=<ID=SAR,Number=.,Type=Integer,Description="Number of alternate observations on the reverse strand"> | |
| ##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> | |
| ##INFO=<ID=SAP,Number=.,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> | |
| ##INFO=<ID=AB,Number=.,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> | |
| ##INFO=<ID=ABP,Number=.,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> | |
| ##INFO=<ID=RUN,Number=.,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> | |
| ##INFO=<ID=RPP,Number=.,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> | |
| ##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> | |
| ##INFO=<ID=RPL,Number=.,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> | |
| ##INFO=<ID=RPR,Number=.,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> | |
| ##INFO=<ID=EPP,Number=.,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> | |
| ##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> | |
| ##INFO=<ID=DPRA,Number=.,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> | |
| ##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> | |
| ##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> | |
| ##INFO=<ID=TYPE,Number=.,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> | |
| ##INFO=<ID=CIGAR,Number=.,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> | |
| ##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> | |
| ##INFO=<ID=MEANALT,Number=.,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> | |
| ##INFO=<ID=LEN,Number=.,Type=Integer,Description="allele length"> | |
| ##INFO=<ID=MQM,Number=.,Type=Float,Description="Mean mapping quality of observed alternate alleles"> | |
| ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> | |
| ##INFO=<ID=PAIRED,Number=.,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> | |
| ##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> | |
| ##INFO=<ID=technology.ILLUMINA,Number=.,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA"> | |
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> | |
| ##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> | |
| ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> | |
| ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> | |
| ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> | |
| ##FORMAT=<ID=AO,Number=.,Type=Integer,Description="Alternate allele observation count"> | |
| ##FORMAT=<ID=QA,Number=.,Type=Integer,Description="Sum of quality of the alternate observations"> | |
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample_A Sample_B Sample_C Sample_D Sample_E Sample_F Sample_G Sample_H Sample_I Sample_J | |
| 12 2813 . G A 1273.14 . SAP=144.282;EPP=144.282;SRR=7;DPB=466.0;MQMR=31.8262;DP=466;PAO=0.0;RPP=152.842;RPR=69.0;PAIRED=0.0;ODDS=0.546204;MEANALT=1.0;MQM=30.1739;SAF=68;PAIREDR=0.0;EPPR=805.356;SAR=1;NS=129;RPL=0.0;technology.ILLUMINA=1.0;RO=397;AC=27;AB=0.803922;SRF=390;AF=0.104651;GTI=15;AO=69;AN=258;ABP=43.9277;SRP=805.356;DPRA=0.940793;RPPR=865.085;PQA=0.0;QR=15506;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=2749;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. 0/0:5:5:187:0:0:0.0,-1.50515,-17.204 ./. ./. ./. ./. ./. | |
| 12 10002883 . C A 145.029 . SAP=3.17734;EPP=23.2217;SRR=472;DPB=899.0;MQMR=46.4255;DP=899;PAO=0.0;RPP=3.17734;RPR=6.0;PAIRED=0.0;ODDS=1.07079;MEANALT=1.0;MQM=45.3077;SAF=6;PAIREDR=0.0;EPPR=1626.95;SAR=7;NS=142;RPL=7.0;technology.ILLUMINA=1.0;RO=886;AC=3;AB=0.6875;SRF=414;AF=0.0105634;GTI=2;AO=13;AN=284;ABP=7.89611;SRP=11.255;DPRA=1.1761;RPPR=3.49067;PQA=0.0;QR=30572;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=388;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 20113144 . C T 382.097 . SAP=4.9405;EPP=4.9405;SRR=2502;DPB=4707.0;MQMR=50.4192;DP=4707;PAO=0.0;RPP=42.0968;RPR=0.0;PAIRED=0.0;ODDS=0.590743;MEANALT=1.0;MQM=46.5;SAF=7;PAIREDR=0.0;EPPR=49.2634;SAR=11;NS=560;RPL=18.0;technology.ILLUMINA=1.0;RO=4688;AC=3;AB=0.45;SRF=2186;AF=0.00267857;GTI=0;AO=18;AN=1120;ABP=3.87889;SRP=49.2634;DPRA=1.59131;RPPR=10182.9;PQA=0.0;QR=172698;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=666;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/0:3:3:119:0:0:0.0,-0.90309,-11.1067 0/0:3:3:117:0:0:0.0,-0.90309,-10.92 ./. ./. 0/0:2:2:68:0:0:0.0,-0.60206,-6.46 ./. 0/0:8:8:251:0:0:0.0,-2.40824,-22.9038 ./. 0/0:9:9:321:0:0:0.0,-2.70927,-29.2467 | |
| 12 30116217 . G C 67.8003 . SAP=18.2106;EPP=18.2106;SRR=0;DPB=67.0;MQMR=57.1833;DP=67;PAO=0.0;RPP=18.2106;RPR=7.0;PAIRED=0.0;ODDS=2.70796;MEANALT=1.0;MQM=30.0;SAF=7;PAIREDR=0.0;EPPR=124.758;SAR=0;NS=41;RPL=0.0;technology.ILLUMINA=1.0;RO=60;AC=5;AB=1.0;SRF=60;AF=0.0609756;GTI=7;AO=7;AN=82;ABP=18.2106;SRP=133.299;DPRA=0.84;RPPR=124.758;PQA=0.0;QR=2331;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=284;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:2:2:79:0:0:0.0,-0.60206,-7.505 ./. ./. 0/0:4:4:148:0:0:0.0,-1.20412,-13.69 ./. ./. ./. 0/0:2:2:77:0:0:0.0,-0.60206,-7.315 ./. ./. | |
| 12 40119560 . G A 4322.4 . SAP=372.161;EPP=372.161;SRR=0;DPB=170.0;MQMR=0.0;DP=170;PAO=0.0;RPP=372.161;RPR=0.0;PAIRED=0.0;ODDS=11.4438;MEANALT=1.0;MQM=59.6824;SAF=0;PAIREDR=0.0;EPPR=0.0;SAR=170;NS=100;RPL=170.0;technology.ILLUMINA=1.0;RO=0;AC=200;AB=0.0;SRF=0;AF=1.0;GTI=0;AO=170;AN=200;ABP=0.0;SRP=0.0;DPRA=0.0;RPPR=0.0;PQA=0.0;QR=0;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=6110;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. 1/1:2:0:0:2:71:-6.745,-0.60206,0.0 ./. ./. ./. ./. | |
| 12 50123996 . G T 124.666 . SAP=61.6401;EPP=61.6401;SRR=14;DPB=47.0;MQMR=60.0;DP=47;PAO=0.0;RPP=61.6401;RPR=27.0;PAIRED=0.0;ODDS=1.03673;MEANALT=1.0;MQM=60.0;SAF=0;PAIREDR=0.0;EPPR=9.95901;SAR=27;NS=35;RPL=0.0;technology.ILLUMINA=1.0;RO=20;AC=32;AB=0.0;SRF=6;AF=0.457143;GTI=1;AO=27;AN=70;ABP=0.0;SRP=9.95901;DPRA=1.56037;RPPR=46.4397;PQA=0.0;QR=697;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=877;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 60124084 . C A 110.857 . SAP=50.7827;EPP=50.7827;SRR=18;DPB=78.0;MQMR=59.4821;DP=78;PAO=0.0;RPP=50.7827;RPR=0.0;PAIRED=0.0;ODDS=0.653797;MEANALT=1.0;MQM=60.0;SAF=22;PAIREDR=0.0;EPPR=15.5738;SAR=0;NS=57;RPL=22.0;technology.ILLUMINA=1.0;RO=56;AC=19;AB=0.695652;SRF=38;AF=0.166667;GTI=11;AO=22;AN=114;ABP=10.6577;SRP=18.5208;DPRA=1.39256;RPPR=116.082;PQA=0.0;QR=1941;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=739;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. 1/1:2:0:0:2:68:-6.46,-0.60206,0.0 ./. ./. ./. ./. ./. ./. ./. | |
| 12 70124366 . G A 391.055 . SAP=9.32731;EPP=9.32731;SRR=1459;DPB=2979.0;MQMR=60.0;DP=2979;PAO=0.0;RPP=50.7827;RPR=0.0;PAIRED=0.0;ODDS=3.06339;MEANALT=1.0;MQM=60.0;SAF=15;PAIREDR=0.0;EPPR=6.3068;SAR=7;NS=557;RPL=22.0;technology.ILLUMINA=1.0;RO=2957;AC=8;AB=1.0;SRF=1498;AF=0.00718133;GTI=13;AO=22;AN=1114;ABP=50.7827;SRP=4.12725;DPRA=0.510568;RPPR=6303.03;PQA=0.0;QR=112006;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=864;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:10:10:338:0:0:0.0,-3.0103,-30.758 0/0:20:20:750:0:0:0.0,-6.0206,-67.875 ./. 0/0:2:2:65:0:0:0.0,-0.60206,-6.175 0/0:9:9:295:0:0:0.0,-2.70927,-26.8778 0/0:5:5:193:0:0:0.0,-1.50515,-17.756 0/0:1:1:32:0:0:0.0,-0.30103,-3.2 0/0:14:14:537:0:0:0.0,-4.21442,-48.7136 0/0:2:2:78:0:0:0.0,-0.60206,-7.41 0/0:14:14:434:0:0:0.0,-4.21442,-39.37 | |
| 12 80124457 . A G 186.293 . SAP=152.842;EPP=152.842;SRR=0;DPB=329.0;MQMR=60.0;DP=329;PAO=0.0;RPP=152.842;RPR=0.0;PAIRED=0.0;ODDS=0.022514;MEANALT=1.0;MQM=60.0;SAF=69;PAIREDR=0.0;EPPR=567.593;SAR=0;NS=184;RPL=69.0;technology.ILLUMINA=1.0;RO=260;AC=80;AB=0.0;SRF=260;AF=0.217391;GTI=2;AO=69;AN=368;ABP=0.0;SRP=567.593;DPRA=0.930417;RPPR=567.593;PQA=0.0;QR=10250;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=2667;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 90126100 . C T 1107.03 . SAP=7.18621;EPP=7.18621;SRR=1909;DPB=4325.0;MQMR=60.0;DP=4325;PAO=0.0;RPP=115.927;RPR=52.0;PAIRED=0.0;ODDS=4.00764;MEANALT=1.0;MQM=60.0;SAF=31;PAIREDR=0.0;EPPR=30.843;SAR=21;NS=569;RPL=0.0;technology.ILLUMINA=1.0;RO=4272;AC=8;AB=0.722222;SRF=2363;AF=0.00702988;GTI=3;AO=52;AN=1138;ABP=33.8935;SRP=107.78;DPRA=1.18716;RPPR=8348.69;PQA=0.0;QR=156873;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=1831;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:14:14:480:0:0:0.0,-4.21442,-43.5429 0/0:9:9:303:0:0:0.0,-2.70927,-27.6067 0/0:12:12:408:0:0:0.0,-3.61236,-37.06 0/0:2:2:70:0:0:0.0,-0.60206,-6.65 0/0:18:18:570:0:0:0.0,-5.41854,-51.6167 0/0:1:1:33:0:0:0.0,-0.30103,-3.3 ./. 0/0:19:19:650:0:0:0.0,-5.71957,-58.8421 0/0:9:9:301:0:0:0.0,-2.70927,-27.4244 0/0:14:14:489:0:0:0.0,-4.21442,-44.3593 | |
| 12 100127575 . G T 56.0599 . SAP=7.35324;EPP=7.35324;SRR=0;DPB=2.0;MQMR=0.0;DP=2;PAO=0.0;RPP=7.35324;RPR=2.0;PAIRED=0.0;ODDS=5.29832;MEANALT=1.0;MQM=39.0;SAF=2;PAIREDR=0.0;EPPR=0.0;SAR=0;NS=1;RPL=0.0;technology.ILLUMINA=1.0;RO=0;AC=2;AB=0.0;SRF=0;AF=1.0;GTI=0;AO=2;AN=2;ABP=0.0;SRP=0.0;DPRA=0.0;RPPR=0.0;PQA=0.0;QR=0;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=78;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 110127613 . A G 46.6986 . SAP=13.8677;EPP=13.8677;SRR=1918;DPB=3766.0;MQMR=41.3026;DP=3766;PAO=0.0;RPP=13.8677;RPR=5.0;PAIRED=0.0;ODDS=10.2055;MEANALT=1.0;MQM=38.6;SAF=5;PAIREDR=0.0;EPPR=6.61364;SAR=0;NS=380;RPL=0.0;technology.ILLUMINA=1.0;RO=3761;AC=1;AB=0.444444;SRF=1843;AF=0.00131579;GTI=0;AO=5;AN=760;ABP=3.25157;SRP=6.25798;DPRA=2.38855;RPPR=8152.56;PQA=0.0;QR=136142;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=198;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:22:22:811:0:0:0.0,-6.62266,-73.3586 0/0:15:15:554:0:0:0.0,-4.51545,-50.2293 0/0:10:10:343:0:0:0.0,-3.0103,-31.213 0/0:13:13:453:0:0:0.0,-3.91339,-41.1185 0/0:8:8:275:0:0:0.0,-2.40824,-25.0938 ./. 0/0:3:3:100:0:0:0.0,-0.90309,-9.33333 0/0:12:12:444:0:0:0.0,-3.61236,-40.33 ./. 0/0:19:19:693:0:0:0.0,-5.71957,-62.7347 | |
| 12 120127684 . A C 42.6222 . SAP=11.6962;EPP=11.6962;SRR=2196;DPB=2203.0;MQMR=38.8707;DP=2203;PAO=0.0;RPP=11.6962;RPR=0.0;PAIRED=0.0;ODDS=8.21565;MEANALT=1.0;MQM=38.25;SAF=0;PAIREDR=0.0;EPPR=4771.56;SAR=4;NS=366;RPL=4.0;technology.ILLUMINA=1.0;RO=2196;AC=1;AB=1.0;SRF=0;AF=0.00136612;GTI=1;AO=4;AN=732;ABP=11.6962;SRP=4771.56;DPRA=0.663938;RPPR=4771.56;PQA=0.0;QR=87210;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=159;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:21:21:799:0:0:0.0,-6.32163,-72.2905 0/0:8:8:309:0:0:0.0,-2.40824,-28.1963 0/0:14:14:549:0:0:0.0,-4.21442,-49.8021 0/0:8:8:318:0:0:0.0,-2.40824,-29.0175 0/0:12:12:466:0:0:0.0,-3.61236,-42.3283 ./. 0/0:3:3:118:0:0:0.0,-0.90309,-11.0133 0/0:2:2:78:0:0:0.0,-0.60206,-7.41 ./. 0/0:12:11:438:0:0:0.0,-3.31133,-39.4183 | |
| 12 130133529 . A G 93.0536 . SAP=165.871;EPP=165.871;SRR=443;DPB=519.0;MQMR=60.0;DP=519;PAO=0.0;RPP=165.871;RPR=75.0;PAIRED=0.0;ODDS=0.860598;MEANALT=1.0;MQM=60.0;SAF=0;PAIREDR=0.0;EPPR=958.478;SAR=75;NS=264;RPL=0.0;technology.ILLUMINA=1.0;RO=444;AC=16;AB=0.0;SRF=1;AF=0.030303;GTI=33;AO=75;AN=528;ABP=0.0;SRP=958.478;DPRA=0.918754;RPPR=967.144;PQA=0.0;QR=15643;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=2546;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:7:7:240:0:0:0.0,-2.10721,-21.9429 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2:2:70:0:0:0.0,-0.60206,-6.65 | |
| 12 140135601 . G A 326.356 . SAP=37.7539;EPP=37.7539;SRR=0;DPB=19.0;MQMR=57.0;DP=19;PAO=0.0;RPP=37.7539;RPR=16.0;PAIRED=0.0;ODDS=2.67078;MEANALT=1.0;MQM=49.375;SAF=0;PAIREDR=0.0;EPPR=9.52472;SAR=16;NS=8;RPL=0.0;technology.ILLUMINA=1.0;RO=3;AC=13;AB=0.0;SRF=3;AF=0.8125;GTI=3;AO=16;AN=16;ABP=0.0;SRP=9.52472;DPRA=0.0;RPPR=9.52472;PQA=0.0;QR=118;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=585;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 150135642 . G A 73.5902 . SAP=13.8677;EPP=13.8677;SRR=15;DPB=22.0;MQMR=47.4118;DP=22;PAO=0.0;RPP=13.8677;RPR=0.0;PAIRED=0.0;ODDS=1.87048;MEANALT=1.0;MQM=48.0;SAF=0;PAIREDR=0.0;EPPR=9.26925;SAR=5;NS=8;RPL=5.0;technology.ILLUMINA=1.0;RO=17;AC=1;AB=1.0;SRF=2;AF=0.0625;GTI=1;AO=5;AN=16;ABP=13.8677;SRP=24.5973;DPRA=2.05882;RPPR=18.4661;PQA=0.0;QR=647;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=200;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. 0/0:3:3:97:0:0:0.0,-0.90309,-9.05333 ./. ./. ./. ./. ./. | |
| 12 160135677 . G A 379.219 . SAP=39.9253;EPP=39.9253;SRR=4;DPB=22.0;MQMR=43.4;DP=22;PAO=0.0;RPP=39.9253;RPR=0.0;PAIRED=0.0;ODDS=2.62295;MEANALT=1.0;MQM=49.0;SAF=0;PAIREDR=0.0;EPPR=6.91895;SAR=17;NS=7;RPL=17.0;technology.ILLUMINA=1.0;RO=5;AC=12;AB=0.0;SRF=1;AF=0.857143;GTI=2;AO=17;AN=14;ABP=0.0;SRP=6.91895;DPRA=0.0;RPPR=13.8677;PQA=0.0;QR=171;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=648;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. 0/1:4:4:134:0:0:0.0,-1.20412,-12.395 ./. ./. ./. ./. ./. | |
| 12 170139035 . T C 183.848 . SAP=50.7827;EPP=50.7827;SRR=0;DPB=149.0;MQMR=43.7953;DP=149;PAO=0.0;RPP=50.7827;RPR=0.0;PAIRED=0.0;ODDS=0.346304;MEANALT=1.0;MQM=45.9545;SAF=22;PAIREDR=0.0;EPPR=278.787;SAR=0;NS=104;RPL=22.0;technology.ILLUMINA=1.0;RO=127;AC=17;AB=1.0;SRF=127;AF=0.0817308;GTI=31;AO=22;AN=208;ABP=50.7827;SRP=278.787;DPRA=0.886522;RPPR=278.787;PQA=0.0;QR=4738;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=817;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. 0/0:5:5:179:0:0:0.0,-1.50515,-16.468 ./. ./. ./. ./. ./. ./. | |
| 12 180141579 . T C 9092.15 . SAP=3.21494;EPP=3.37411;SRR=546;DPB=1140.0;MQMR=60.0;DP=1140;PAO=0.0;RPP=789.652;RPR=5.0;PAIRED=0.0;ODDS=0.671793;MEANALT=1.0;MQM=60.0;SAF=194;PAIREDR=0.0;EPPR=274.771;SAR=188;NS=383;RPL=377.0;technology.ILLUMINA=1.0;RO=758;AC=168;AB=0.0;SRF=212;AF=0.219321;GTI=1;AO=382;AN=766;ABP=0.0;SRP=322.589;DPRA=1.78777;RPPR=1488.09;PQA=0.0;QR=29113;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=15079;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/0:6:6:219:0:0:0.0,-1.80618,-20.075 ./. 0/0:1:1:41:0:0:0.0,-0.30103,-4.1 ./. ./. ./. 0/0:5:5:171:0:0:0.0,-1.50515,-15.732 ./. ./. | |
| 12 190141599 . G A 76.4376 . SAP=3.12459;EPP=3.12459;SRR=732;DPB=929.0;MQMR=60.0;DP=929;PAO=0.0;RPP=44.2683;RPR=0.0;PAIRED=0.0;ODDS=0.352249;MEANALT=1.0;MQM=60.0;SAF=10;PAIREDR=0.0;EPPR=735.384;SAR=9;NS=349;RPL=19.0;technology.ILLUMINA=1.0;RO=910;AC=8;AB=0.0;SRF=178;AF=0.0114613;GTI=2;AO=19;AN=698;ABP=0.0;SRP=735.384;DPRA=1.19359;RPPR=1979.05;PQA=0.0;QR=35149;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=715;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/0:2:2:82:0:0:0.0,-0.60206,-7.79 ./. 0/0:1:1:41:0:0:0.0,-0.30103,-4.1 ./. ./. ./. ./. ./. ./. | |
| 12 200142965 . C T 60.1221 . SAP=20.3821;EPP=20.3821;SRR=1;DPB=49.0;MQMR=60.0;DP=49;PAO=0.0;RPP=20.3821;RPR=8.0;PAIRED=0.0;ODDS=2.02136;MEANALT=1.0;MQM=60.0;SAF=8;PAIREDR=0.0;EPPR=53.9075;SAR=0;NS=31;RPL=0.0;technology.ILLUMINA=1.0;RO=41;AC=6;AB=1.0;SRF=40;AF=0.0967742;GTI=9;AO=8;AN=62;ABP=20.3821;SRP=83.5666;DPRA=0.813008;RPPR=47.552;PQA=0.0;QR=1497;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=296;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. 0/0:4:4:135:0:0:0.0,-1.20412,-12.4875 ./. 0/0:2:2:65:0:0:0.0,-0.60206,-6.175 ./. ./. ./. ./. ./. | |
| 12 210143013 . G A 32.6998 . SAP=18.2106;EPP=18.2106;SRR=0;DPB=41.0;MQMR=60.0;DP=41;PAO=0.0;RPP=18.2106;RPR=0.0;PAIRED=0.0;ODDS=1.50059;MEANALT=1.0;MQM=60.0;SAF=7;PAIREDR=0.0;EPPR=76.8404;SAR=0;NS=27;RPL=7.0;technology.ILLUMINA=1.0;RO=34;AC=5;AB=1.0;SRF=34;AF=0.0925926;GTI=8;AO=7;AN=54;ABP=18.2106;SRP=76.8404;DPRA=0.905882;RPPR=76.8404;PQA=0.0;QR=1193;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=239;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. 0/0:2:2:68:0:0:0.0,-0.60206,-6.46 ./. 0/0:1:1:33:0:0:0.0,-0.30103,-3.3 ./. ./. ./. ./. ./. | |
| 12 220143180 . C G 90.2746 . SAP=29.068;EPP=21.1059;SRR=0;DPB=24.0;MQMR=60.0;DP=24;PAO=0.0;RPP=21.1059;RPR=1.0;PAIRED=0.0;ODDS=3.02422;MEANALT=1.0;MQM=58.8333;SAF=12;PAIREDR=0.0;EPPR=29.068;SAR=0;NS=18;RPL=11.0;technology.ILLUMINA=1.0;RO=12;AC=18;AB=0.0;SRF=12;AF=0.5;GTI=0;AO=12;AN=36;ABP=0.0;SRP=29.068;DPRA=1.0;RPPR=29.068;PQA=0.0;QR=397;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=432;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 230143188 . A G 90.2675 . SAP=31.2394;EPP=23.2217;SRR=0;DPB=23.0;MQMR=60.0;DP=23;PAO=0.0;RPP=23.2217;RPR=1.0;PAIRED=0.0;ODDS=2.34308;MEANALT=1.0;MQM=58.9231;SAF=13;PAIREDR=0.0;EPPR=24.725;SAR=0;NS=18;RPL=12.0;technology.ILLUMINA=1.0;RO=10;AC=36;AB=0.0;SRF=10;AF=1.0;GTI=0;AO=13;AN=36;ABP=0.0;SRP=24.725;DPRA=1.04;RPPR=24.725;PQA=0.0;QR=327;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=425;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 240143258 . G A 356.877 . SAP=42.0968;EPP=42.0968;SRR=4;DPB=23.0;MQMR=55.8;DP=23;PAO=0.0;RPP=42.0968;RPR=18.0;PAIRED=0.0;ODDS=2.10162;MEANALT=1.0;MQM=60.0;SAF=0;PAIREDR=0.0;EPPR=13.8677;SAR=18;NS=14;RPL=0.0;technology.ILLUMINA=1.0;RO=5;AC=25;AB=0.0;SRF=1;AF=0.892857;GTI=3;AO=18;AN=28;ABP=0.0;SRP=6.91895;DPRA=0.0;RPPR=6.91895;PQA=0.0;QR=167;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=636;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 250143272 . T C 544.684 . SAP=50.7827;EPP=50.7827;SRR=0;DPB=22.0;MQMR=0.0;DP=22;PAO=0.0;RPP=50.7827;RPR=22.0;PAIRED=0.0;ODDS=9.39424;MEANALT=1.0;MQM=59.6818;SAF=0;PAIREDR=0.0;EPPR=0.0;SAR=22;NS=14;RPL=0.0;technology.ILLUMINA=1.0;RO=0;AC=28;AB=0.0;SRF=0;AF=1.0;GTI=0;AO=22;AN=28;ABP=0.0;SRP=0.0;DPRA=0.0;RPPR=0.0;PQA=0.0;QR=0;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=771;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 260143337 . T C 1607.88 . SAP=12.9715;EPP=131.265;SRR=13;DPB=76.0;MQMR=60.0;DP=76;PAO=0.0;RPP=15.4532;RPR=41.0;PAIRED=0.0;ODDS=18.4175;MEANALT=1.0;MQM=59.8889;SAF=40;PAIREDR=0.0;EPPR=7.18621;SAR=23;NS=51;RPL=22.0;technology.ILLUMINA=1.0;RO=13;AC=102;AB=0.0;SRF=0;AF=1.0;GTI=0;AO=63;AN=102;ABP=0.0;SRP=31.2394;DPRA=1.33269;RPPR=7.18621;PQA=0.0;QR=480;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=2319;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 270143378 . C T 53.8725 . SAP=3.0103;EPP=3.0103;SRR=47;DPB=88.0;MQMR=59.975;DP=88;PAO=0.0;RPP=20.3821;RPR=0.0;PAIRED=0.0;ODDS=0.837425;MEANALT=1.0;MQM=60.0;SAF=4;PAIREDR=0.0;EPPR=8.33041;SAR=4;NS=52;RPL=8.0;technology.ILLUMINA=1.0;RO=80;AC=6;AB=1.0;SRF=33;AF=0.0576923;GTI=10;AO=8;AN=104;ABP=20.3821;SRP=8.33041;DPRA=0.766667;RPPR=176.728;PQA=0.0;QR=2981;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=263;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 280143874 . C T 48.6313 . SAP=16.0391;EPP=16.0391;SRR=0;DPB=17.0;MQMR=60.0;DP=17;PAO=0.0;RPP=16.0391;RPR=0.0;PAIRED=0.0;ODDS=2.19315;MEANALT=1.0;MQM=60.0;SAF=6;PAIREDR=0.0;EPPR=26.8965;SAR=0;NS=11;RPL=6.0;technology.ILLUMINA=1.0;RO=11;AC=3;AB=1.0;SRF=11;AF=0.136364;GTI=3;AO=6;AN=22;ABP=16.0391;SRP=26.8965;DPRA=1.45455;RPPR=26.8965;PQA=0.0;QR=375;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=210;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 290148203 . C T 1382.36 . SAP=6.81824;EPP=6.81824;SRR=1101;DPB=2894.0;MQMR=60.0;DP=2894;PAO=0.0;RPP=152.842;RPR=69.0;PAIRED=0.0;ODDS=0.380215;MEANALT=1.0;MQM=60.0;SAF=40;PAIREDR=0.0;EPPR=300.499;SAR=29;NS=511;RPL=0.0;technology.ILLUMINA=1.0;RO=2824;AC=14;AB=0.0;SRF=1723;AF=0.0136986;GTI=0;AO=69;AN=1022;ABP=0.0;SRP=300.499;DPRA=1.75858;RPPR=6135.25;PQA=0.0;QR=105000;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=2559;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/0:6:6:203:0:0:0.0,-1.80618,-18.6083 ./. 0/0:19:19:703:0:0:0.0,-5.71957,-63.64 0/0:7:7:273:0:0:0.0,-2.10721,-24.96 0/0:5:5:200:0:0:0.0,-1.50515,-18.4 ./. 0/0:21:21:650:0:0:0.0,-6.32163,-58.8095 ./. 0/0:2:2:67:0:0:0.0,-0.60206,-6.365 | |
| 12 300148244 . C A 20383.8 . SAP=11.9941;EPP=8.55644;SRR=1263;DPB=3411.0;MQMR=60.0;DP=3411;PAO=0.0;RPP=1597.28;RPR=6.0;PAIRED=0.0;ODDS=3.50901;MEANALT=1.0;MQM=59.996;SAF=351;PAIREDR=0.0;EPPR=5763.93;SAR=407;NS=539;RPL=752.0;technology.ILLUMINA=1.0;RO=2653;AC=180;AB=0.0;SRF=1390;AF=0.166976;GTI=1;AO=758;AN=1078;ABP=0.0;SRP=16.2118;DPRA=1.43054;RPPR=16.2118;PQA=0.0;QR=102831;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=29622;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/0:6:6:224:0:0:0.0,-1.80618,-20.5333 0/0:3:3:115:0:0:0.0,-0.90309,-10.7333 0/0:32:32:1195:0:0:0.0,-9.63296,-107.923 0/0:7:7:246:0:0:0.0,-2.10721,-22.4914 0/0:5:5:195:0:0:0.0,-1.50515,-17.94 ./. 0/0:25:25:944:0:0:0.0,-7.52575,-85.3376 ./. 0/0:8:8:265:0:0:0.0,-2.40824,-24.1813 | |
| 12 310148272 . G A 6678.41 . SAP=867.447;EPP=867.447;SRR=1285;DPB=2994.0;MQMR=60.0;DP=2994;PAO=0.0;RPP=893.314;RPR=0.0;PAIRED=0.0;ODDS=0.48864;MEANALT=1.0;MQM=59.9927;SAF=3;PAIREDR=0.0;EPPR=4.49268;SAR=407;NS=527;RPL=410.0;technology.ILLUMINA=1.0;RO=2584;AC=124;AB=0.0;SRF=1299;AF=0.117647;GTI=18;AO=410;AN=1054;ABP=0.0;SRP=3.17501;DPRA=0.902336;RPPR=5493.15;PQA=0.0;QR=95328;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=15360;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/0:6:6:229:0:0:0.0,-1.80618,-20.9917 0/0:3:3:121:0:0:0.0,-0.90309,-11.2933 0/0:34:34:1161:0:0:0.0,-10.235,-104.831 0/0:6:6:188:0:0:0.0,-1.80618,-17.2333 0/0:4:4:117:0:0:0.0,-1.20412,-10.8225 ./. 0/0:27:27:1066:0:0:0.0,-8.12781,-96.3348 ./. 0/0:9:9:325:0:0:0.0,-2.70927,-29.6111 | |
| 12 320150852 . T C 1392.28 . SAP=202.786;EPP=202.786;SRR=62;DPB=154.0;MQMR=60.0;DP=154;PAO=0.0;RPP=202.786;RPR=92.0;PAIRED=0.0;ODDS=0.209186;MEANALT=1.0;MQM=59.8696;SAF=92;PAIREDR=0.0;EPPR=23.184;SAR=0;NS=89;RPL=0.0;technology.ILLUMINA=1.0;RO=62;AC=56;AB=0.857143;SRF=0;AF=0.314607;GTI=21;AO=92;AN=178;ABP=41.7866;SRP=137.642;DPRA=1.9923;RPPR=23.184;PQA=0.0;QR=2437;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=3341;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 330150898 . G A 1924.31 . SAP=185.513;EPP=25.2185;SRR=42;DPB=139.0;MQMR=60.0;DP=139;PAO=0.0;RPP=22.3561;RPR=30.0;PAIRED=0.0;ODDS=5.14097;MEANALT=1.0;MQM=59.8636;SAF=87;PAIREDR=0.0;EPPR=55.1682;SAR=1;NS=82;RPL=58.0;technology.ILLUMINA=1.0;RO=51;AC=76;AB=0.0;SRF=9;AF=0.463415;GTI=0;AO=88;AN=164;ABP=0.0;SRP=49.3776;DPRA=1.99794;RPPR=105.24;PQA=0.0;QR=2051;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=3483;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 340150902 . G A 34.406 . SAP=13.8677;EPP=13.8677;SRR=44;DPB=143.0;MQMR=59.7029;DP=143;PAO=0.0;RPP=13.8677;RPR=0.0;PAIRED=0.0;ODDS=1.42364;MEANALT=1.0;MQM=60.0;SAF=5;PAIREDR=0.0;EPPR=25.7321;SAR=0;NS=84;RPL=5.0;technology.ILLUMINA=1.0;RO=138;AC=3;AB=1.0;SRF=94;AF=0.0178571;GTI=5;AO=5;AN=168;ABP=13.8677;SRP=42.3486;DPRA=0.978261;RPPR=237.215;PQA=0.0;QR=5395;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=201;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 350150922 . G A 7013.96 . SAP=692.011;EPP=174.209;SRR=32;DPB=2105.0;MQMR=59.1923;DP=2105;PAO=0.0;RPP=187.044;RPR=253.0;PAIRED=0.0;ODDS=0.559589;MEANALT=1.0;MQM=58.997;SAF=332;PAIREDR=0.0;EPPR=3444.79;SAR=5;NS=513;RPL=84.0;technology.ILLUMINA=1.0;RO=1768;AC=154;AB=0.0;SRF=1736;AF=0.150097;GTI=2;AO=337;AN=1026;ABP=0.0;SRP=3569.26;DPRA=1.05085;RPPR=3712.99;PQA=0.0;QR=69740;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=13191;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:7:7:259:0:0:0.0,-2.10721,-23.68 ./. 0/0:5:5:185:0:0:0.0,-1.50515,-17.02 0/0:26:26:945:0:0:0.0,-7.82678,-85.4135 ./. ./. 0/0:2:2:80:0:0:0.0,-0.60206,-7.6 0/0:20:20:738:0:0:0.0,-6.0206,-66.789 0/0:18:18:680:0:0:0.0,-5.41854,-61.5778 0/0:9:9:341:0:0:0.0,-2.70927,-31.0689 | |
| 12 360151082 . C T 343.958 . SAP=79.0118;EPP=79.0118;SRR=0;DPB=346.0;MQMR=59.8103;DP=346;PAO=0.0;RPP=79.0118;RPR=0.0;PAIRED=0.0;ODDS=1.95865;MEANALT=1.0;MQM=57.7143;SAF=35;PAIREDR=0.0;EPPR=678.338;SAR=0;NS=205;RPL=35.0;technology.ILLUMINA=1.0;RO=311;AC=23;AB=1.0;SRF=311;AF=0.0560976;GTI=43;AO=35;AN=410;ABP=79.0118;SRP=678.338;DPRA=0.890535;RPPR=678.338;PQA=0.0;QR=10981;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=1317;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 370151098 . G A 326.943 . SAP=11.5903;EPP=181.071;SRR=452;DPB=821.0;MQMR=59.9973;DP=821;PAO=0.0;RPP=11.5903;RPR=50.0;PAIRED=0.0;ODDS=1.52352;MEANALT=1.0;MQM=59.4268;SAF=32;PAIREDR=0.0;EPPR=1607.73;SAR=50;NS=352;RPL=32.0;technology.ILLUMINA=1.0;RO=739;AC=38;AB=0.0;SRF=287;AF=0.0539773;GTI=25;AO=82;AN=704;ABP=0.0;SRP=83.008;DPRA=0.776725;RPPR=83.008;PQA=0.0;QR=24712;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=2870;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 380151109 . C T 375.893 . SAP=13.8677;EPP=176.728;SRR=458;DPB=818.0;MQMR=59.9973;DP=818;PAO=0.0;RPP=13.8677;RPR=50.0;PAIRED=0.0;ODDS=2.72273;MEANALT=1.0;MQM=59.65;SAF=30;PAIREDR=0.0;EPPR=1605.56;SAR=50;NS=350;RPL=30.0;technology.ILLUMINA=1.0;RO=738;AC=38;AB=0.0;SRF=280;AF=0.0542857;GTI=25;AO=80;AN=700;ABP=0.0;SRP=96.2365;DPRA=0.75388;RPPR=96.2365;PQA=0.0;QR=26132;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=2937;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 390151245 . A T 373.704 . SAP=10.2485;EPP=10.2485;SRR=2114;DPB=4135.0;MQMR=58.8943;DP=4135;PAO=0.0;RPP=68.1545;RPR=0.0;PAIRED=0.0;ODDS=2.08347;MEANALT=1.0;MQM=57.1333;SAF=10;PAIREDR=0.0;EPPR=15.3932;SAR=20;NS=570;RPL=30.0;technology.ILLUMINA=1.0;RO=4105;AC=10;AB=0.0;SRF=1991;AF=0.00877193;GTI=2;AO=30;AN=1140;ABP=0.0;SRP=11.0133;DPRA=0.587785;RPPR=7758.55;PQA=0.0;QR=160016;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=1187;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:7:7:276:0:0:0.0,-2.10721,-25.2343 0/0:18:18:675:0:0:0.0,-5.41854,-61.125 0/0:25:25:982:0:0:0.0,-7.52575,-88.7728 0/0:10:10:389:0:0:0.0,-3.0103,-35.399 0/0:15:15:573:0:0:0.0,-4.51545,-51.952 0/0:10:10:365:0:0:0.0,-3.0103,-33.215 0/0:1:1:39:0:0:0.0,-0.30103,-3.9 0/0:6:6:242:0:0:0.0,-1.80618,-22.1833 0/0:17:17:672:0:0:0.0,-5.11751,-60.8753 0/0:6:6:214:0:0:0.0,-1.80618,-19.6167 | |
| 12 400151250 . T C 655.416 . SAP=7.09778;EPP=7.09778;SRR=2120;DPB=4140.0;MQMR=58.868;DP=4140;PAO=0.0;RPP=76.8404;RPR=0.0;PAIRED=0.0;ODDS=0.504965;MEANALT=1.0;MQM=57.4118;SAF=13;PAIREDR=0.0;EPPR=5.52878;SAR=21;NS=571;RPL=34.0;technology.ILLUMINA=1.0;RO=4105;AC=9;AB=0.820513;SRF=1985;AF=0.00788091;GTI=8;AO=34;AN=1142;ABP=37.8095;SRP=12.651;DPRA=0.913785;RPPR=8052.96;PQA=0.0;QR=159622;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=1337;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:7:7:276:0:0:0.0,-2.10721,-25.2343 0/0:18:18:657:0:0:0.0,-5.41854,-59.495 0/0:25:25:940:0:0:0.0,-7.52575,-84.976 0/0:10:10:381:0:0:0.0,-3.0103,-34.671 0/0:17:17:649:0:0:0.0,-5.11751,-58.7918 0/0:10:10:367:0:0:0.0,-3.0103,-33.397 0/0:1:1:38:0:0:0.0,-0.30103,-3.8 0/0:7:7:272:0:0:0.0,-2.10721,-24.8686 0/0:16:16:590:0:0:0.0,-4.81648,-53.4688 0/0:6:6:200:0:0:0.0,-1.80618,-18.3333 | |
| 12 410153015 . T G 2382.19 . SAP=333.074;EPP=324.445;SRR=0;DPB=1053.0;MQMR=60.0;DP=1053;PAO=0.0;RPP=324.445;RPR=151.0;PAIRED=0.0;ODDS=0.0265501;MEANALT=1.0;MQM=60.0;SAF=152;PAIREDR=0.0;EPPR=1940.0;SAR=0;NS=391;RPL=1.0;technology.ILLUMINA=1.0;RO=900;AC=72;AB=0.95;SRF=900;AF=0.0920716;GTI=54;AO=152;AN=782;ABP=178.9;SRP=1957.34;DPRA=0.895281;RPPR=1940.0;PQA=0.0;QR=35282;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=5872;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:9:9:345:0:0:0.0,-2.70927,-31.4333 0/0:2:2:79:0:0:0.0,-0.60206,-7.505 0/0:11:11:419:0:0:0.0,-3.31133,-38.0909 0/0:6:6:228:0:0:0.0,-1.80618,-20.9 0/0:9:9:351:0:0:0.0,-2.70927,-31.98 0/0:4:4:159:0:0:0.0,-1.20412,-14.7075 ./. 0/0:2:2:77:0:0:0.0,-0.60206,-7.315 ./. 0/0:15:15:557:0:0:0.0,-4.51545,-50.5013 | |
| 12 420154021 . C T 144.682 . SAP=3.0103;EPP=33.4109;SRR=126;DPB=250.0;MQMR=57.3475;DP=250;PAO=0.0;RPP=3.0103;RPR=7.0;PAIRED=0.0;ODDS=1.01405;MEANALT=1.0;MQM=60.0;SAF=7;PAIREDR=0.0;EPPR=515.478;SAR=7;NS=85;RPL=7.0;technology.ILLUMINA=1.0;RO=236;AC=7;AB=1.0;SRF=110;AF=0.0411765;GTI=11;AO=14;AN=170;ABP=33.4109;SRP=5.3658;DPRA=0.661017;RPPR=5.3658;PQA=0.0;QR=7720;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=440;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 430154059 . T G 3811.88 . SAP=304.845;EPP=304.845;SRR=2;DPB=141.0;MQMR=60.0;DP=141;PAO=0.0;RPP=304.845;RPR=0.0;PAIRED=0.0;ODDS=3.98375;MEANALT=1.0;MQM=54.4029;SAF=0;PAIREDR=0.0;EPPR=7.35324;SAR=139;NS=62;RPL=139.0;technology.ILLUMINA=1.0;RO=2;AC=124;AB=0.0;SRF=0;AF=1.0;GTI=1;AO=139;AN=124;ABP=0.0;SRP=7.35324;DPRA=2.31667;RPPR=7.35324;PQA=0.0;QR=77;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=5433;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 440154074 . A G 3883.09 . SAP=304.845;EPP=304.845;SRR=2;DPB=141.0;MQMR=60.0;DP=141;PAO=0.0;RPP=304.845;RPR=0.0;PAIRED=0.0;ODDS=3.98375;MEANALT=1.0;MQM=54.4029;SAF=0;PAIREDR=0.0;EPPR=7.35324;SAR=139;NS=62;RPL=139.0;technology.ILLUMINA=1.0;RO=2;AC=124;AB=0.0;SRF=0;AF=1.0;GTI=1;AO=139;AN=124;ABP=0.0;SRP=7.35324;DPRA=2.31667;RPPR=7.35324;PQA=0.0;QR=77;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=5509;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 450154141 . A G 3225.56 . SAP=320.045;EPP=320.045;SRR=0;DPB=148.0;MQMR=60.0;DP=148;PAO=0.0;RPP=320.045;RPR=0.0;PAIRED=0.0;ODDS=4.56906;MEANALT=1.0;MQM=39.9521;SAF=146;PAIREDR=0.0;EPPR=7.35324;SAR=0;NS=53;RPL=146.0;technology.ILLUMINA=1.0;RO=2;AC=106;AB=0.0;SRF=2;AF=1.0;GTI=1;AO=146;AN=106;ABP=0.0;SRP=7.35324;DPRA=2.86275;RPPR=7.35324;PQA=0.0;QR=64;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=4911;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 460154223 . C T 3323.16 . SAP=333.074;EPP=333.074;SRR=3;DPB=155.0;MQMR=60.0;DP=155;PAO=0.0;RPP=333.074;RPR=152.0;PAIRED=0.0;ODDS=0.215012;MEANALT=1.0;MQM=60.0;SAF=0;PAIREDR=0.0;EPPR=9.52472;SAR=152;NS=60;RPL=0.0;technology.ILLUMINA=1.0;RO=3;AC=120;AB=0.0;SRF=0;AF=1.0;GTI=1;AO=152;AN=120;ABP=0.0;SRP=9.52472;DPRA=1.74713;RPPR=9.52472;PQA=0.0;QR=107;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=5084;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 470154249 . G A 125.777 . SAP=35.5824;EPP=35.5824;SRR=197;DPB=212.0;MQMR=60.0;DP=212;PAO=0.0;RPP=35.5824;RPR=15.0;PAIRED=0.0;ODDS=1.46354;MEANALT=1.0;MQM=54.4667;SAF=0;PAIREDR=0.0;EPPR=430.79;SAR=15;NS=74;RPL=0.0;technology.ILLUMINA=1.0;RO=197;AC=8;AB=1.0;SRF=0;AF=0.0540541;GTI=13;AO=15;AN=148;ABP=35.5824;SRP=430.79;DPRA=0.628173;RPPR=430.79;PQA=0.0;QR=6688;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=517;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. 0/0:1:1:32:0:0:0.0,-0.30103,-3.2 ./. ./. ./. | |
| 12 480154254 . A G 5133.89 . SAP=498.106;EPP=498.106;SRR=4;DPB=232.0;MQMR=60.0;DP=232;PAO=0.0;RPP=498.106;RPR=228.0;PAIRED=0.0;ODDS=1.20981;MEANALT=1.0;MQM=59.6184;SAF=0;PAIREDR=0.0;EPPR=11.6962;SAR=228;NS=75;RPL=0.0;technology.ILLUMINA=1.0;RO=4;AC=150;AB=0.0;SRF=0;AF=1.0;GTI=2;AO=228;AN=150;ABP=0.0;SRP=11.6962;DPRA=2.375;RPPR=11.6962;PQA=0.0;QR=138;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=7823;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. 1/1:1:1:31:0:0:0.0,-0.30103,-3.1 ./. ./. ./. | |
| 12 490154342 . G A 10234.6 . SAP=316.799;EPP=205.484;SRR=12;DPB=474.0;MQMR=48.3065;DP=474;PAO=0.0;RPP=701.339;RPR=388.0;PAIRED=0.0;ODDS=0.0986252;MEANALT=1.0;MQM=44.7621;SAF=328;PAIREDR=0.0;EPPR=30.4689;SAR=84;NS=110;RPL=24.0;technology.ILLUMINA=1.0;RO=62;AC=196;AB=0.0;SRF=50;AF=0.890909;GTI=9;AO=412;AN=220;ABP=0.0;SRP=53.5846;DPRA=1.56796;RPPR=83.705;PQA=0.0;QR=2163;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=13670;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1:1:35:0:0:0.0,-0.30103,-3.5 | |
| 12 500154354 . G A 843.583 . SAP=40.5935;EPP=31.2394;SRR=219;DPB=602.0;MQMR=42.4226;DP=602;PAO=0.0;RPP=3.67845;RPR=24.0;PAIRED=0.0;ODDS=4.23781;MEANALT=1.0;MQM=46.3269;SAF=41;PAIREDR=0.0;EPPR=232.739;SAR=11;NS=115;RPL=28.0;technology.ILLUMINA=1.0;RO=549;AC=22;AB=0.0;SRF=330;AF=0.0956522;GTI=0;AO=52;AN=230;ABP=0.0;SRP=51.7438;DPRA=0.893884;RPPR=150.342;PQA=0.0;QR=18339;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=1742;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1:1:41:0:0:0.0,-0.30103,-4.1 | |
| 12 510154375 . C G 13716.3 . SAP=27.5072;EPP=1114.8;SRR=22;DPB=593.0;MQMR=49.0494;DP=593;PAO=0.0;RPP=27.5072;RPR=218.0;PAIRED=0.0;ODDS=0.15393;MEANALT=1.0;MQM=41.9355;SAF=294;PAIREDR=0.0;EPPR=178.9;SAR=218;NS=118;RPL=294.0;technology.ILLUMINA=1.0;RO=81;AC=190;AB=0.0;SRF=59;AF=0.805085;GTI=9;AO=512;AN=236;ABP=0.0;SRP=39.7109;DPRA=2.28453;RPPR=39.7109;PQA=0.0;QR=2865;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=18191;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 520164811 . G A 73.6504 . SAP=20.3821;EPP=20.3821;SRR=54;DPB=62.0;MQMR=60.0;DP=62;PAO=0.0;RPP=20.3821;RPR=8.0;PAIRED=0.0;ODDS=1.83633;MEANALT=1.0;MQM=60.0;SAF=8;PAIREDR=0.0;EPPR=120.27;SAR=0;NS=49;RPL=0.0;technology.ILLUMINA=1.0;RO=54;AC=4;AB=1.0;SRF=0;AF=0.0408163;GTI=5;AO=8;AN=98;ABP=20.3821;SRP=120.27;DPRA=1.66667;RPPR=120.27;PQA=0.0;QR=1847;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=308;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 530164817 . T C 83.1434 . SAP=20.3821;EPP=20.3821;SRR=54;DPB=62.0;MQMR=60.0;DP=62;PAO=0.0;RPP=20.3821;RPR=8.0;PAIRED=0.0;ODDS=2.29685;MEANALT=1.0;MQM=60.0;SAF=8;PAIREDR=0.0;EPPR=120.27;SAR=0;NS=49;RPL=0.0;technology.ILLUMINA=1.0;RO=54;AC=4;AB=1.0;SRF=0;AF=0.0408163;GTI=5;AO=8;AN=98;ABP=20.3821;SRP=120.27;DPRA=1.66667;RPPR=120.27;PQA=0.0;QR=1848;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=318;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 540164900 . G A 49.2443 . SAP=36.4176;EPP=36.4176;SRR=53;DPB=180.0;MQMR=60.0;DP=180;PAO=0.0;RPP=19.3799;RPR=20.0;PAIRED=0.0;ODDS=0.272635;MEANALT=1.0;MQM=60.0;SAF=23;PAIREDR=0.0;EPPR=117.224;SAR=3;NS=124;RPL=6.0;technology.ILLUMINA=1.0;RO=154;AC=8;AB=0.0;SRF=101;AF=0.0322581;GTI=14;AO=26;AN=248;ABP=0.0;SRP=35.4978;DPRA=0.994228;RPPR=6.62002;PQA=0.0;QR=6010;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=1036;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1:1:40:0:0:0.0,-0.30103,-4.0 | |
| 12 550164952 . G C 202.558 . SAP=50.7827;EPP=9.32731;SRR=0;DPB=112.0;MQMR=60.0;DP=112;PAO=0.0;RPP=9.32731;RPR=7.0;PAIRED=0.0;ODDS=0.992975;MEANALT=1.0;MQM=60.0;SAF=22;PAIREDR=0.0;EPPR=45.5712;SAR=0;NS=87;RPL=15.0;technology.ILLUMINA=1.0;RO=90;AC=16;AB=1.0;SRF=90;AF=0.091954;GTI=29;AO=22;AN=174;ABP=50.7827;SRP=198.443;DPRA=1.08472;RPPR=45.5712;PQA=0.0;QR=3146;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=716;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1:1:35:0:0:0.0,-0.30103,-3.5 | |
| 12 560165095 . C T 83.9385 . SAP=24.725;EPP=24.725;SRR=81;DPB=91.0;MQMR=60.0;DP=91;PAO=0.0;RPP=24.725;RPR=10.0;PAIRED=0.0;ODDS=1.76172;MEANALT=1.0;MQM=60.0;SAF=10;PAIREDR=0.0;EPPR=178.9;SAR=0;NS=70;RPL=0.0;technology.ILLUMINA=1.0;RO=81;AC=5;AB=1.0;SRF=0;AF=0.0357143;GTI=8;AO=10;AN=140;ABP=24.725;SRP=178.9;DPRA=1.60494;RPPR=178.9;PQA=0.0;QR=2771;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=373;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. 0/0:4:4:127:0:0:0.0,-1.20412,-11.7475 ./. 0/0:1:1:35:0:0:0.0,-0.30103,-3.5 0/0:1:1:35:0:0:0.0,-0.30103,-3.5 ./. ./. ./. | |
| 12 570165122 . C T 301.961 . SAP=5.18177;EPP=3.55317;SRR=92;DPB=108.0;MQMR=60.0;DP=108;PAO=0.0;RPP=29.6108;RPR=15.0;PAIRED=0.0;ODDS=2.53234;MEANALT=1.0;MQM=60.0;SAF=10;PAIREDR=0.0;EPPR=87.981;SAR=6;NS=74;RPL=1.0;technology.ILLUMINA=1.0;RO=92;AC=5;AB=1.0;SRF=0;AF=0.0337838;GTI=7;AO=16;AN=148;ABP=37.7539;SRP=202.786;DPRA=2.4;RPPR=87.981;PQA=0.0;QR=3414;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=627;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. 0/0:8:8:269:0:0:0.0,-2.40824,-24.5463 ./. 0/0:2:2:69:0:0:0.0,-0.60206,-6.555 0/0:2:2:71:0:0:0.0,-0.60206,-6.745 ./. ./. ./. | |
| 12 580165402 . T C 32.5323 . SAP=4.9405;EPP=4.9405;SRR=0;DPB=54.0;MQMR=59.8333;DP=54;PAO=0.0;RPP=42.0968;RPR=18.0;PAIRED=0.0;ODDS=2.23842;MEANALT=1.0;MQM=59.8333;SAF=7;PAIREDR=0.0;EPPR=64.7766;SAR=11;NS=44;RPL=0.0;technology.ILLUMINA=1.0;RO=36;AC=30;AB=0.0;SRF=36;AF=0.340909;GTI=0;AO=18;AN=88;ABP=0.0;SRP=81.1833;DPRA=0.966667;RPPR=64.7766;PQA=0.0;QR=1421;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=633;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/0:1:1:41:0:0:0.0,-0.30103,-4.1 ./. ./. ./. ./. ./. ./. 0/0:3:3:110:0:0:0.0,-0.90309,-10.2667 ./. | |
| 12 590165430 . G A 148.475 . SAP=8.07707;EPP=3.94093;SRR=0;DPB=55.0;MQMR=60.0;DP=55;PAO=0.0;RPP=32.8939;RPR=2.0;PAIRED=0.0;ODDS=4.88681;MEANALT=1.0;MQM=59.4286;SAF=7;PAIREDR=0.0;EPPR=76.8404;SAR=14;NS=46;RPL=19.0;technology.ILLUMINA=1.0;RO=34;AC=36;AB=0.0;SRF=34;AF=0.391304;GTI=0;AO=21;AN=92;ABP=0.0;SRP=76.8404;DPRA=0.960784;RPPR=76.8404;PQA=0.0;QR=1154;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=785;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/0:1:1:35:0:0:0.0,-0.30103,-3.5 ./. ./. ./. ./. ./. ./. 0/0:2:2:59:0:0:0.0,-0.60206,-5.605 ./. | |
| 12 600165543 . T G 9100.02 . SAP=26.5564;EPP=23.5216;SRR=41;DPB=373.0;MQMR=60.0;DP=373;PAO=0.0;RPP=706.672;RPR=2.0;PAIRED=0.0;ODDS=36.0563;MEANALT=1.0;MQM=60.0;SAF=136;PAIREDR=0.0;EPPR=83.5666;SAR=196;NS=117;RPL=330.0;technology.ILLUMINA=1.0;RO=41;AC=234;AB=0.0;SRF=0;AF=1.0;GTI=2;AO=332;AN=234;ABP=0.0;SRP=92.0407;DPRA=3.31707;RPPR=83.5666;PQA=0.0;QR=1608;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=12284;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 1/1:1:1:37:0:0:0.0,-0.30103,-3.7 ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 610167158 . G T 172.716 . SAP=48.6112;EPP=48.6112;SRR=116;DPB=137.0;MQMR=60.0;DP=137;PAO=0.0;RPP=48.6112;RPR=21.0;PAIRED=0.0;ODDS=0.0844852;MEANALT=1.0;MQM=60.0;SAF=0;PAIREDR=0.0;EPPR=254.901;SAR=21;NS=95;RPL=0.0;technology.ILLUMINA=1.0;RO=116;AC=9;AB=0.875;SRF=0;AF=0.0473684;GTI=6;AO=21;AN=190;ABP=32.3252;SRP=254.901;DPRA=2.0295;RPPR=254.901;PQA=0.0;QR=4395;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=704;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:1:1:38:0:0:0.0,-0.30103,-3.8 ./. ./. ./. 0/1:6:0:0:6:206:-18.8833,-1.80618,0.0 ./. ./. ./. ./. 0/0:1:1:38:0:0:0.0,-0.30103,-3.8 | |
| 12 620167250 . T A 100.772 . SAP=13.8677;EPP=13.8677;SRR=0;DPB=5.0;MQMR=0.0;DP=5;PAO=0.0;RPP=13.8677;RPR=0.0;PAIRED=0.0;ODDS=7.83534;MEANALT=1.0;MQM=60.0;SAF=5;PAIREDR=0.0;EPPR=0.0;SAR=0;NS=2;RPL=5.0;technology.ILLUMINA=1.0;RO=0;AC=4;AB=0.0;SRF=0;AF=1.0;GTI=0;AO=5;AN=4;ABP=0.0;SRP=0.0;DPRA=0.0;RPPR=0.0;PQA=0.0;QR=0;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=155;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 630168028 . C A 36.8503 . SAP=22.5536;EPP=22.5536;SRR=0;DPB=67.0;MQMR=60.0;DP=67;PAO=0.0;RPP=22.5536;RPR=0.0;PAIRED=0.0;ODDS=1.28302;MEANALT=1.0;MQM=60.0;SAF=9;PAIREDR=0.0;EPPR=120.42;SAR=0;NS=53;RPL=9.0;technology.ILLUMINA=1.0;RO=58;AC=6;AB=0.9;SRF=58;AF=0.0566038;GTI=5;AO=9;AN=106;ABP=16.9077;SRP=128.956;DPRA=1.37427;RPPR=120.42;PQA=0.0;QR=1953;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=307;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 640168217 . C A 51.5874 . SAP=6.91895;EPP=6.91895;SRR=25;DPB=46.0;MQMR=60.0;DP=46;PAO=0.0;RPP=13.8677;RPR=5.0;PAIRED=0.0;ODDS=2.1401;MEANALT=1.0;MQM=60.0;SAF=1;PAIREDR=0.0;EPPR=7.30028;SAR=4;NS=25;RPL=0.0;technology.ILLUMINA=1.0;RO=41;AC=4;AB=1.0;SRF=16;AF=0.08;GTI=5;AO=5;AN=50;ABP=13.8677;SRP=7.30028;DPRA=0.640244;RPPR=92.0407;PQA=0.0;QR=1551;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=198;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 650168895 . G T 579.912 . SAP=213.643;EPP=213.643;SRR=0;DPB=408.0;MQMR=60.0;DP=408;PAO=0.0;RPP=213.643;RPR=97.0;PAIRED=0.0;ODDS=1.54973;MEANALT=1.0;MQM=60.0;SAF=97;PAIREDR=0.0;EPPR=678.338;SAR=0;NS=229;RPL=0.0;technology.ILLUMINA=1.0;RO=311;AC=104;AB=0.0;SRF=311;AF=0.227074;GTI=0;AO=97;AN=458;ABP=0.0;SRP=678.338;DPRA=1.06165;RPPR=678.338;PQA=0.0;QR=12047;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=3793;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 660169843 . C T 77.6101 . SAP=16.0391;EPP=16.0391;SRR=0;DPB=1580.0;MQMR=60.0;DP=1580;PAO=0.0;RPP=16.0391;RPR=6.0;PAIRED=0.0;ODDS=5.87599;MEANALT=1.0;MQM=60.0;SAF=6;PAIREDR=0.0;EPPR=3224.05;SAR=0;NS=403;RPL=0.0;technology.ILLUMINA=1.0;RO=1574;AC=1;AB=0.545455;SRF=1574;AF=0.00124069;GTI=0;AO=6;AN=806;ABP=3.20771;SRP=3420.91;DPRA=2.81836;RPPR=3224.05;PQA=0.0;QR=62458;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=224;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/1:11:5:196:6:224:-19.8866,0.0,-17.3853 0/0:1:1:40:0:0:0.0,-0.30103,-4.0 0/0:24:24:940:0:0:0.0,-7.22472,-84.9917 0/0:12:12:463:0:0:0.0,-3.61236,-42.0558 0/0:9:9:352:0:0:0.0,-2.70927,-32.0711 0/0:7:7:278:0:0:0.0,-2.10721,-25.4171 ./. 0/0:40:40:1517:0:0:0.0,-12.0412,-136.909 0/0:3:3:118:0:0:0.0,-0.90309,-11.0133 0/0:9:9:355:0:0:0.0,-2.70927,-32.3444 | |
| 12 670169944 . C A 129.803 . SAP=31.2394;EPP=31.2394;SRR=4;DPB=46.0;MQMR=59.1212;DP=46;PAO=0.0;RPP=31.2394;RPR=0.0;PAIRED=0.0;ODDS=2.16804;MEANALT=1.0;MQM=60.0;SAF=13;PAIREDR=0.0;EPPR=74.6689;SAR=0;NS=25;RPL=13.0;technology.ILLUMINA=1.0;RO=33;AC=5;AB=0.8125;SRF=29;AF=0.1;GTI=4;AO=13;AN=50;ABP=16.582;SRP=44.1367;DPRA=2.13333;RPPR=44.1367;PQA=0.0;QR=1241;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=437;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. 0/0:3:3:120:0:0:0.0,-0.90309,-11.2 ./. ./. ./. ./. ./. | |
| 12 680174262 . T C 102.44 . SAP=20.3821;EPP=20.3821;SRR=1;DPB=10.0;MQMR=60.0;DP=10;PAO=0.0;RPP=20.3821;RPR=8.0;PAIRED=0.0;ODDS=3.76286;MEANALT=1.0;MQM=42.0;SAF=0;PAIREDR=0.0;EPPR=5.18177;SAR=8;NS=9;RPL=0.0;technology.ILLUMINA=1.0;RO=1;AC=18;AB=0.0;SRF=0;AF=1.0;GTI=0;AO=8;AN=18;ABP=0.0;SRP=5.18177;DPRA=1.14286;RPPR=5.18177;PQA=0.0;QR=33;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=201;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 690174316 . G T 4547.55 . SAP=153.624;EPP=153.624;SRR=1;DPB=151.0;MQMR=60.0;DP=151;PAO=0.0;RPP=328.731;RPR=0.0;PAIRED=0.0;ODDS=4.10153;MEANALT=1.0;MQM=42.26;SAF=24;PAIREDR=0.0;EPPR=5.18177;SAR=126;NS=70;RPL=150.0;technology.ILLUMINA=1.0;RO=1;AC=140;AB=0.0;SRF=0;AF=1.0;GTI=0;AO=150;AN=140;ABP=0.0;SRP=5.18177;DPRA=2.17391;RPPR=5.18177;PQA=0.0;QR=40;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=5691;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 700191117 . A G 75.3338 . SAP=3.32051;EPP=5.80219;SRR=247;DPB=449.0;MQMR=60.0;DP=449;PAO=0.0;RPP=5.80219;RPR=5.0;PAIRED=0.0;ODDS=1.80836;MEANALT=1.0;MQM=60.0;SAF=3;PAIREDR=0.0;EPPR=11.6765;SAR=4;NS=246;RPL=2.0;technology.ILLUMINA=1.0;RO=442;AC=4;AB=1.0;SRF=195;AF=0.00813008;GTI=6;AO=7;AN=492;ABP=18.2106;SRP=16.2946;DPRA=0.958145;RPPR=773.421;PQA=0.0;QR=15401;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=269;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/0:3:3:87:0:0:0.0,-0.90309,-8.12 ./. 0/0:4:4:157:0:0:0.0,-1.20412,-14.5225 ./. 0/0:1:1:21:0:0:0.0,-0.30103,-2.1 ./. ./. 0/0:1:1:31:0:0:0.0,-0.30103,-3.1 ./. | |
| 12 710191173 . G T 149.078 . SAP=102.898;EPP=102.898;SRR=426;DPB=795.0;MQMR=60.0;DP=795;PAO=0.0;RPP=102.898;RPR=46.0;PAIRED=0.0;ODDS=0.0450937;MEANALT=1.0;MQM=60.0;SAF=0;PAIREDR=0.0;EPPR=23.9567;SAR=46;NS=325;RPL=0.0;technology.ILLUMINA=1.0;RO=749;AC=29;AB=0.419355;SRF=323;AF=0.0446154;GTI=13;AO=46;AN=650;ABP=8.26386;SRP=33.7675;DPRA=1.58379;RPPR=1535.3;PQA=0.0;QR=27369;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=1517;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/0:6:6:214:0:0:0.0,-1.80618,-19.6167 ./. ./. 0/0:1:1:30:0:0:0.0,-0.30103,-3.0 0/0:1:1:37:0:0:0.0,-0.30103,-3.7 ./. ./. 0/0:1:1:39:0:0:0.0,-0.30103,-3.9 0/0:1:1:35:0:0:0.0,-0.30103,-3.5 | |
| 12 720191177 . C A 36.0033 . SAP=42.0968;EPP=42.0968;SRR=171;DPB=411.0;MQMR=60.0;DP=411;PAO=0.0;RPP=42.0968;RPR=0.0;PAIRED=0.0;ODDS=0.365095;MEANALT=1.0;MQM=60.0;SAF=18;PAIREDR=0.0;EPPR=10.5745;SAR=0;NS=221;RPL=18.0;technology.ILLUMINA=1.0;RO=393;AC=3;AB=0.8;SRF=222;AF=0.00678733;GTI=16;AO=18;AN=442;ABP=10.8276;SRP=17.3818;DPRA=1.35092;RPPR=747.218;PQA=0.0;QR=14242;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=581;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/0:3:3:101:0:0:0.0,-0.90309,-9.42667 ./. ./. 0/0:1:1:28:0:0:0.0,-0.30103,-2.8 ./. ./. 0/0:4:4:146:0:0:0.0,-1.20412,-13.505 ./. 0/0:1:1:34:0:0:0.0,-0.30103,-3.4 | |
| 12 730191265 . C A 254.522 . SAP=94.2121;EPP=94.2121;SRR=60;DPB=164.0;MQMR=59.959;DP=164;PAO=0.0;RPP=94.2121;RPR=0.0;PAIRED=0.0;ODDS=0.0412781;MEANALT=1.0;MQM=60.0;SAF=42;PAIREDR=0.0;EPPR=13.2625;SAR=0;NS=106;RPL=42.0;technology.ILLUMINA=1.0;RO=122;AC=23;AB=0.827586;SRF=62;AF=0.108491;GTI=14;AO=42;AN=212;ABP=30.0414;SRP=3.0815;DPRA=1.62597;RPPR=167.045;PQA=0.0;QR=4361;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=1296;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 740205985 . A T 58.1044 . SAP=24.725;EPP=24.725;SRR=672;DPB=682.0;MQMR=60.0;DP=682;PAO=0.0;RPP=24.725;RPR=0.0;PAIRED=0.0;ODDS=0.596884;MEANALT=1.0;MQM=60.0;SAF=0;PAIREDR=0.0;EPPR=1410.59;SAR=10;NS=322;RPL=10.0;technology.ILLUMINA=1.0;RO=672;AC=5;AB=1.0;SRF=0;AF=0.00776398;GTI=9;AO=10;AN=644;ABP=22.5536;SRP=1462.24;DPRA=0.78373;RPPR=1410.59;PQA=0.0;QR=26597;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=382;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:15:15:594:0:0:0.0,-4.51545,-53.856 0/0:1:1:38:0:0:0.0,-0.30103,-3.8 ./. 0/0:6:6:228:0:0:0.0,-1.80618,-20.9 0/0:4:4:162:0:0:0.0,-1.20412,-14.985 0/0:1:1:40:0:0:0.0,-0.30103,-4.0 ./. 0/0:11:11:411:0:0:0.0,-3.31133,-37.3636 ./. ./. | |
| 12 750207211 . G A 112.809 . SAP=48.6112;EPP=48.6112;SRR=89;DPB=110.0;MQMR=59.809;DP=110;PAO=0.0;RPP=48.6112;RPR=21.0;PAIRED=0.0;ODDS=0.292056;MEANALT=1.0;MQM=60.0;SAF=0;PAIREDR=0.0;EPPR=196.271;SAR=21;NS=89;RPL=0.0;technology.ILLUMINA=1.0;RO=89;AC=15;AB=1.0;SRF=0;AF=0.0842697;GTI=29;AO=21;AN=178;ABP=46.4397;SRP=196.271;DPRA=1.07654;RPPR=196.271;PQA=0.0;QR=3054;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=714;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. 0/0:2:2:65:0:0:0.0,-0.60206,-6.175 0/0:2:2:69:0:0:0.0,-0.60206,-6.555 ./. | |
| 12 760208256 . T C 41.4156 . SAP=3.0103;EPP=3.0103;SRR=1722;DPB=3565.0;MQMR=57.8379;DP=3565;PAO=0.0;RPP=16.0391;RPR=6.0;PAIRED=0.0;ODDS=5.86687;MEANALT=1.0;MQM=60.0;SAF=3;PAIREDR=0.0;EPPR=5.58812;SAR=3;NS=548;RPL=0.0;technology.ILLUMINA=1.0;RO=3559;AC=2;AB=0.277778;SRF=1837;AF=0.00182482;GTI=0;AO=6;AN=1096;ABP=10.7311;SRP=11.0793;DPRA=2.27019;RPPR=7515.66;PQA=0.0;QR=127855;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=221;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:7:7:263:0:0:0.0,-2.10721,-24.0457 ./. 0/0:5:5:171:0:0:0.0,-1.50515,-15.732 0/0:16:16:570:0:0:0.0,-4.81648,-51.6563 0/0:14:14:496:0:0:0.0,-4.21442,-44.9943 0/0:7:7:231:0:0:0.0,-2.10721,-21.12 0/0:2:2:69:0:0:0.0,-0.60206,-6.555 0/0:16:16:583:0:0:0.0,-4.81648,-52.8344 0/0:7:7:234:0:0:0.0,-2.10721,-21.3943 0/0:6:6:193:0:0:0.0,-1.80618,-17.6917 | |
| 12 770208785 . A G 249.325 . SAP=22.5536;EPP=22.5536;SRR=0;DPB=9.0;MQMR=0.0;DP=9;PAO=0.0;RPP=22.5536;RPR=0.0;PAIRED=0.0;ODDS=8.44379;MEANALT=1.0;MQM=59.7778;SAF=0;PAIREDR=0.0;EPPR=0.0;SAR=9;NS=5;RPL=9.0;technology.ILLUMINA=1.0;RO=0;AC=10;AB=0.0;SRF=0;AF=1.0;GTI=0;AO=9;AN=10;ABP=0.0;SRP=0.0;DPRA=0.0;RPPR=0.0;PQA=0.0;QR=0;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=346;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 780208830 . A G 3537.94 . SAP=354.789;EPP=72.4974;SRR=0;DPB=267.0;MQMR=58.381;DP=267;PAO=0.0;RPP=72.4974;RPR=117.0;PAIRED=0.0;ODDS=5.06108;MEANALT=1.0;MQM=58.0494;SAF=162;PAIREDR=0.0;EPPR=44.8887;SAR=0;NS=87;RPL=45.0;technology.ILLUMINA=1.0;RO=105;AC=94;AB=0.0;SRF=105;AF=0.54023;GTI=0;AO=162;AN=174;ABP=0.0;SRP=231.015;DPRA=1.31307;RPPR=44.8887;PQA=0.0;QR=3608;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=5683;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 790208962 . G A 122.362 . SAP=24.725;EPP=24.725;SRR=344;DPB=354.0;MQMR=59.8285;DP=354;PAO=0.0;RPP=24.725;RPR=0.0;PAIRED=0.0;ODDS=4.3152;MEANALT=1.0;MQM=59.7;SAF=0;PAIREDR=0.0;EPPR=741.336;SAR=10;NS=132;RPL=10.0;technology.ILLUMINA=1.0;RO=344;AC=3;AB=1.0;SRF=0;AF=0.0113636;GTI=3;AO=10;AN=264;ABP=24.725;SRP=749.997;DPRA=1.25;RPPR=741.336;PQA=0.0;QR=13414;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=385;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1:1:38:0:0:0.0,-0.30103,-3.8 ./. | |
| 12 800208982 . G A 9801.15 . SAP=80.7213;EPP=80.7213;SRR=2762;DPB=5850.0;MQMR=59.9836;DP=5850;PAO=0.0;RPP=819.484;RPR=376.0;PAIRED=0.0;ODDS=0.409857;MEANALT=1.0;MQM=59.9335;SAF=246;PAIREDR=0.0;EPPR=4.00202;SAR=130;NS=504;RPL=0.0;technology.ILLUMINA=1.0;RO=5474;AC=83;AB=0.990431;SRF=2712;AF=0.0823413;GTI=59;AO=376;AN=1008;ABP=439.642;SRP=4.00202;DPRA=0.414474;RPPR=11889.7;PQA=0.0;QR=213014;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=14743;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:3:3:114:0:0:0.0,-0.90309,-10.64 ./. 0/0:4:4:145:0:0:0.0,-1.20412,-13.4125 0/0:10:10:389:0:0:0.0,-3.0103,-35.399 ./. ./. 0/0:1:1:40:0:0:0.0,-0.30103,-4.0 ./. 0/0:4:4:161:0:0:0.0,-1.20412,-14.8925 0/0:7:7:254:0:0:0.0,-2.10721,-23.2229 | |
| 12 810209043 . C T 62.3942 . SAP=16.0391;EPP=16.0391;SRR=1139;DPB=3648.0;MQMR=52.2221;DP=3648;PAO=0.0;RPP=16.0391;RPR=0.0;PAIRED=0.0;ODDS=7.60684;MEANALT=1.0;MQM=60.0;SAF=6;PAIREDR=0.0;EPPR=529.84;SAR=0;NS=536;RPL=6.0;technology.ILLUMINA=1.0;RO=3642;AC=1;AB=1.0;SRF=2503;AF=0.000932836;GTI=1;AO=6;AN=1072;ABP=16.0391;SRP=1112.3;DPRA=0.881384;RPPR=6177.29;PQA=0.0;QR=124625;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=214;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:24:24:781:0:0:0.0,-7.22472,-70.6154 0/0:15:15:494:0:0:0.0,-4.51545,-44.7893 0/0:2:2:70:0:0:0.0,-0.60206,-6.65 0/0:7:7:235:0:0:0.0,-2.10721,-21.4857 0/0:20:20:678:0:0:0.0,-6.0206,-61.359 0/0:7:7:216:0:0:0.0,-2.10721,-19.7486 0/0:1:1:35:0:0:0.0,-0.30103,-3.5 0/0:23:23:723:0:0:0.0,-6.92369,-65.3843 0/0:18:18:579:0:0:0.0,-5.41854,-52.4317 0/0:8:8:267:0:0:0.0,-2.40824,-24.3637 | |
| 12 820209053 . T C 38.2983 . SAP=10.8276;EPP=10.8276;SRR=1138;DPB=3615.0;MQMR=52.1568;DP=3615;PAO=0.0;RPP=3.87889;RPR=4.0;PAIRED=0.0;ODDS=0.613128;MEANALT=1.0;MQM=55.0;SAF=8;PAIREDR=0.0;EPPR=190.613;SAR=2;NS=535;RPL=6.0;technology.ILLUMINA=1.0;RO=3604;AC=2;AB=0.285714;SRF=2466;AF=0.00186916;GTI=2;AO=10;AN=1070;ABP=11.386;SRP=1065.6;DPRA=2.17418;RPPR=4842.16;PQA=0.0;QR=123912;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=319;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:23:23:777:0:0:0.0,-6.92369,-70.2678 0/0:15:15:499:0:0:0.0,-4.51545,-45.2427 0/0:2:2:70:0:0:0.0,-0.60206,-6.65 0/0:7:7:235:0:0:0.0,-2.10721,-21.4857 0/0:20:20:667:0:0:0.0,-6.0206,-60.3635 0/0:8:8:256:0:0:0.0,-2.40824,-23.36 0/0:1:1:35:0:0:0.0,-0.30103,-3.5 0/0:24:24:760:0:0:0.0,-7.22472,-68.7167 0/0:18:18:600:0:0:0.0,-5.41854,-54.3333 0/0:7:7:242:0:0:0.0,-2.10721,-22.1257 | |
| 12 830209130 . C T 98.434 . SAP=3.0103;EPP=3.0103;SRR=1280;DPB=2440.0;MQMR=59.9601;DP=2440;PAO=0.0;RPP=24.725;RPR=10.0;PAIRED=0.0;ODDS=0.0298797;MEANALT=1.0;MQM=60.0;SAF=5;PAIREDR=0.0;EPPR=13.0509;SAR=5;NS=373;RPL=0.0;technology.ILLUMINA=1.0;RO=2430;AC=4;AB=1.0;SRF=1150;AF=0.00536193;GTI=6;AO=10;AN=746;ABP=22.5536;SRP=18.1123;DPRA=0.302881;RPPR=5175.97;PQA=0.0;QR=95946;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=363;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 840213753 . C T 32.7296 . SAP=18.2106;EPP=18.2106;SRR=0;DPB=128.0;MQMR=60.0;DP=128;PAO=0.0;RPP=18.2106;RPR=0.0;PAIRED=0.0;ODDS=1.4855;MEANALT=1.0;MQM=60.0;SAF=7;PAIREDR=0.0;EPPR=265.758;SAR=0;NS=97;RPL=7.0;technology.ILLUMINA=1.0;RO=121;AC=6;AB=1.0;SRF=121;AF=0.0309278;GTI=11;AO=7;AN=194;ABP=18.2106;SRP=265.758;DPRA=0.87741;RPPR=265.758;PQA=0.0;QR=4536;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=281;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:2:2:60:0:0:0.0,-0.60206,-5.7 ./. 0/0:1:1:39:0:0:0.0,-0.30103,-3.9 ./. ./. ./. ./. ./. ./. 0/0:6:6:214:0:0:0.0,-1.80618,-19.6167 | |
| 12 850214011 . G T 44.1571 . SAP=18.2106;EPP=18.2106;SRR=50;DPB=57.0;MQMR=60.0;DP=57;PAO=0.0;RPP=18.2106;RPR=0.0;PAIRED=0.0;ODDS=1.86039;MEANALT=1.0;MQM=60.0;SAF=0;PAIREDR=0.0;EPPR=111.584;SAR=7;NS=50;RPL=7.0;technology.ILLUMINA=1.0;RO=50;AC=6;AB=1.0;SRF=0;AF=0.06;GTI=10;AO=7;AN=100;ABP=18.2106;SRP=111.584;DPRA=1.02667;RPPR=111.584;PQA=0.0;QR=2009;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=278;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 860214116 . T C 66.1538 . SAP=24.725;EPP=24.725;SRR=0;DPB=489.0;MQMR=60.0;DP=489;PAO=0.0;RPP=24.725;RPR=0.0;PAIRED=0.0;ODDS=0.416835;MEANALT=1.0;MQM=59.6;SAF=10;PAIREDR=0.0;EPPR=1043.15;SAR=0;NS=225;RPL=10.0;technology.ILLUMINA=1.0;RO=479;AC=5;AB=0.909091;SRF=479;AF=0.0111111;GTI=4;AO=10;AN=450;ABP=19.0002;SRP=1043.15;DPRA=1.01255;RPPR=1043.15;PQA=0.0;QR=16858;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=364;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:9:9:307:0:0:0.0,-2.70927,-27.9711 ./. 0/0:8:8:244:0:0:0.0,-2.40824,-22.265 ./. ./. ./. ./. 0/0:14:14:472:0:0:0.0,-4.21442,-42.8171 ./. 0/0:6:6:205:0:0:0.0,-1.80618,-18.7917 | |
| 12 870214722 . T C 79.4119 . SAP=9.52472;EPP=9.52472;SRR=0;DPB=3.0;MQMR=0.0;DP=3;PAO=0.0;RPP=9.52472;RPR=3.0;PAIRED=0.0;ODDS=7.25998;MEANALT=1.0;MQM=60.0;SAF=3;PAIREDR=0.0;EPPR=0.0;SAR=0;NS=2;RPL=0.0;technology.ILLUMINA=1.0;RO=0;AC=4;AB=0.0;SRF=0;AF=1.0;GTI=0;AO=3;AN=4;ABP=0.0;SRP=0.0;DPRA=0.0;RPPR=0.0;PQA=0.0;QR=0;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=110;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 880219814 . T C 38.2436 . SAP=48.6112;EPP=48.6112;SRR=0;DPB=107.0;MQMR=60.0;DP=107;PAO=0.0;RPP=48.6112;RPR=21.0;PAIRED=0.0;ODDS=0.163769;MEANALT=1.0;MQM=60.0;SAF=21;PAIREDR=0.0;EPPR=189.757;SAR=0;NS=66;RPL=0.0;technology.ILLUMINA=1.0;RO=86;AC=22;AB=0.0;SRF=86;AF=0.166667;GTI=0;AO=21;AN=132;ABP=0.0;SRP=189.757;DPRA=1.22093;RPPR=189.757;PQA=0.0;QR=3299;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=806;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. 0/0:1:1:41:0:0:0.0,-0.30103,-4.1 0/0:5:5:202:0:0:0.0,-1.50515,-18.584 ./. ./. ./. ./. ./. | |
| 12 890221254 . C T 44.8344 . SAP=11.6962;EPP=11.6962;SRR=2183;DPB=2576.0;MQMR=42.7321;DP=2576;PAO=0.0;RPP=11.6962;RPR=0.0;PAIRED=0.0;ODDS=8.04884;MEANALT=1.0;MQM=40.0;SAF=0;PAIREDR=0.0;EPPR=2720.25;SAR=4;NS=516;RPL=4.0;technology.ILLUMINA=1.0;RO=2572;AC=1;AB=1.0;SRF=389;AF=0.000968992;GTI=1;AO=4;AN=1032;ABP=11.6962;SRP=2720.25;DPRA=0.800933;RPPR=5588.04;PQA=0.0;QR=99432;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=164;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/0:9:9:326:0:0:0.0,-2.70927,-29.7022 ./. ./. 0/0:5:5:199:0:0:0.0,-1.50515,-18.308 0/0:1:1:39:0:0:0.0,-0.30103,-3.9 0/0:1:1:41:0:0:0.0,-0.30103,-4.1 0/0:11:11:383:0:0:0.0,-3.31133,-34.8182 0/0:4:4:159:0:0:0.0,-1.20412,-14.7075 0/0:12:12:474:0:0:0.0,-3.61236,-43.055 | |
| 12 900221778 . T C 66.6953 . SAP=3.32051;EPP=10.7656;SRR=613;DPB=1246.0;MQMR=59.8725;DP=1246;PAO=0.0;RPP=3.32051;RPR=3.0;PAIRED=0.0;ODDS=0.404853;MEANALT=1.0;MQM=59.7143;SAF=3;PAIREDR=0.0;EPPR=3.7832;SAR=4;NS=259;RPL=4.0;technology.ILLUMINA=1.0;RO=1239;AC=4;AB=1.0;SRF=626;AF=0.00772201;GTI=7;AO=7;AN=518;ABP=18.2106;SRP=3.30649;DPRA=0.360169;RPPR=2324.86;PQA=0.0;QR=47903;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=259;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 910221932 . C A 92.8243 . SAP=24.725;EPP=24.725;SRR=0;DPB=19.0;MQMR=55.6667;DP=19;PAO=0.0;RPP=24.725;RPR=0.0;PAIRED=0.0;ODDS=0.067756;MEANALT=1.0;MQM=50.0;SAF=10;PAIREDR=0.0;EPPR=14.8328;SAR=0;NS=9;RPL=10.0;technology.ILLUMINA=1.0;RO=9;AC=7;AB=0.666667;SRF=9;AF=0.388889;GTI=2;AO=10;AN=18;ABP=3.73412;SRP=22.5536;DPRA=1.57143;RPPR=14.8328;PQA=0.0;QR=301;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=317;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 920228374 . G A 39.651 . SAP=13.8677;EPP=13.8677;SRR=2837;DPB=3419.0;MQMR=59.7014;DP=3419;PAO=0.0;RPP=13.8677;RPR=0.0;PAIRED=0.0;ODDS=8.00787;MEANALT=1.0;MQM=60.0;SAF=5;PAIREDR=0.0;EPPR=3255.52;SAR=0;NS=556;RPL=5.0;technology.ILLUMINA=1.0;RO=3413;AC=1;AB=0.714286;SRF=576;AF=0.000899281;GTI=0;AO=5;AN=1112;ABP=5.80219;SRP=3255.52;DPRA=1.13863;RPPR=7414.25;PQA=0.0;QR=133045;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=166;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:15:15:599:0:0:0.0,-4.51545,-54.3093 0/0:13:13:516:0:0:0.0,-3.91339,-46.8369 0/0:16:16:636:0:0:0.0,-4.81648,-57.6375 ./. 0/0:1:1:41:0:0:0.0,-0.30103,-4.1 0/0:15:15:507:0:0:0.0,-4.51545,-45.968 ./. 0/0:16:16:571:0:0:0.0,-4.81648,-51.7469 0/0:17:17:677:0:0:0.0,-5.11751,-61.3282 ./. | |
| 12 930228387 . G A 33.7346 . SAP=11.6962;EPP=11.6962;SRR=2821;DPB=2825.0;MQMR=59.6569;DP=2825;PAO=0.0;RPP=11.6962;RPR=0.0;PAIRED=0.0;ODDS=7.73269;MEANALT=1.0;MQM=60.0;SAF=0;PAIREDR=0.0;EPPR=6128.73;SAR=4;NS=548;RPL=4.0;technology.ILLUMINA=1.0;RO=2821;AC=1;AB=0.266667;SRF=0;AF=0.000912409;GTI=0;AO=4;AN=1096;ABP=10.1038;SRP=6128.73;DPRA=2.91993;RPPR=6128.73;PQA=0.0;QR=110820;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=154;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:15:15:572:0:0:0.0,-4.51545,-51.8613 0/0:12:12:445:0:0:0.0,-3.61236,-40.4208 0/0:16:16:634:0:0:0.0,-4.81648,-57.4563 ./. 0/0:1:1:41:0:0:0.0,-0.30103,-4.1 0/0:3:3:117:0:0:0.0,-0.90309,-10.92 ./. 0/0:10:10:387:0:0:0.0,-3.0103,-35.217 0/0:17:17:661:0:0:0.0,-5.11751,-59.8788 ./. | |
| 12 940228420 . A C 88.582 . SAP=11.6962;EPP=11.6962;SRR=1;DPB=5.0;MQMR=60.0;DP=5;PAO=0.0;RPP=11.6962;RPR=4.0;PAIRED=0.0;ODDS=1.80543;MEANALT=1.0;MQM=60.0;SAF=4;PAIREDR=0.0;EPPR=5.18177;SAR=0;NS=2;RPL=0.0;technology.ILLUMINA=1.0;RO=1;AC=4;AB=0.0;SRF=0;AF=1.0;GTI=0;AO=4;AN=4;ABP=0.0;SRP=5.18177;DPRA=4.0;RPPR=5.18177;PQA=0.0;QR=33;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=160;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 950235040 . C T 100.847 . SAP=18.9659;EPP=18.9659;SRR=1034;DPB=2783.0;MQMR=59.7949;DP=2783;PAO=0.0;RPP=52.9542;RPR=23.0;PAIRED=0.0;ODDS=0.249132;MEANALT=1.0;MQM=60.0;SAF=18;PAIREDR=0.0;EPPR=379.764;SAR=5;NS=514;RPL=0.0;technology.ILLUMINA=1.0;RO=2760;AC=10;AB=0.0;SRF=1726;AF=0.00972763;GTI=2;AO=23;AN=1028;ABP=0.0;SRP=379.764;DPRA=0.603571;RPPR=5996.27;PQA=0.0;QR=102147;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=859;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/0:1:1:35:0:0:0.0,-0.30103,-3.5 0/0:3:3:116:0:0:0.0,-0.90309,-10.8267 0/0:2:2:80:0:0:0.0,-0.60206,-7.6 0/0:15:15:575:0:0:0.0,-4.51545,-52.1333 0/0:3:3:109:0:0:0.0,-0.90309,-10.1733 ./. 0/0:9:9:343:0:0:0.0,-2.70927,-31.2511 0/0:9:9:332:0:0:0.0,-2.70927,-30.2489 ./. | |
| 12 960235047 . C T 18788.0 . SAP=4.03769;EPP=4.03769;SRR=714;DPB=2850.0;MQMR=59.8644;DP=2850;PAO=0.0;RPP=1659.84;RPR=763.0;PAIRED=0.0;ODDS=0.000519913;MEANALT=1.0;MQM=59.6016;SAF=372;PAIREDR=0.0;EPPR=454.869;SAR=391;NS=515;RPL=0.0;technology.ILLUMINA=1.0;RO=2087;AC=186;AB=0.885135;SRF=1373;AF=0.180583;GTI=84;AO=763;AN=1030;ABP=193.689;SRP=454.869;DPRA=1.56818;RPPR=4534.87;PQA=0.0;QR=77965;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=27565;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/1:1:1:41:0:0:0.0,-0.30103,-4.1 0/0:3:3:116:0:0:0.0,-0.90309,-10.8267 0/0:2:2:81:0:0:0.0,-0.60206,-7.695 0/0:15:15:565:0:0:0.0,-4.51545,-51.2267 0/0:3:3:119:0:0:0.0,-0.90309,-11.1067 ./. 0/0:9:9:344:0:0:0.0,-2.70927,-31.3422 0/0:10:10:381:0:0:0.0,-3.0103,-34.671 ./. | |
| 12 970235049 . C A 39.7345 . SAP=3.0103;EPP=3.0103;SRR=1112;DPB=2853.0;MQMR=59.8044;DP=2853;PAO=0.0;RPP=11.6962;RPR=4.0;PAIRED=0.0;ODDS=8.32355;MEANALT=1.0;MQM=60.0;SAF=2;PAIREDR=0.0;EPPR=299.892;SAR=2;NS=514;RPL=0.0;technology.ILLUMINA=1.0;RO=2848;AC=1;AB=1.0;SRF=1736;AF=0.000972763;GTI=1;AO=4;AN=1028;ABP=11.6962;SRP=299.892;DPRA=0.720253;RPPR=6187.36;PQA=0.0;QR=106341;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=141;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. 0/0:1:1:41:0:0:0.0,-0.30103,-4.1 0/0:3:3:112:0:0:0.0,-0.90309,-10.4533 0/0:2:2:81:0:0:0.0,-0.60206,-7.695 0/0:15:15:564:0:0:0.0,-4.51545,-51.136 0/0:3:3:116:0:0:0.0,-0.90309,-10.8267 ./. 0/0:9:9:334:0:0:0.0,-2.70927,-30.4311 0/0:10:10:393:0:0:0.0,-3.0103,-35.763 ./. | |
| 12 980235115 . C T 8446.9 . SAP=924.03;EPP=873.573;SRR=1;DPB=2070.0;MQMR=60.0;DP=2070;PAO=0.0;RPP=907.053;RPR=434.0;PAIRED=0.0;ODDS=0.0192126;MEANALT=1.0;MQM=60.0;SAF=436;PAIREDR=0.0;EPPR=320.264;SAR=4;NS=503;RPL=6.0;technology.ILLUMINA=1.0;RO=1630;AC=114;AB=0.970874;SRF=1629;AF=0.11332;GTI=62;AO=440;AN=1006;ABP=399.736;SRP=3533.83;DPRA=1.27749;RPPR=317.669;PQA=0.0;QR=60804;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=16565;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:8:8:319:0:0:0.0,-2.40824,-29.1088 0/0:1:1:35:0:0:0.0,-0.30103,-3.5 0/0:1:1:33:0:0:0.0,-0.30103,-3.3 0/0:2:2:62:0:0:0.0,-0.60206,-5.89 0/0:9:9:298:0:0:0.0,-2.70927,-27.1511 0/0:4:4:143:0:0:0.0,-1.20412,-13.2275 ./. 0/0:6:6:182:0:0:0.0,-1.80618,-16.6833 0/0:13:13:475:0:0:0.0,-3.91339,-43.1154 0/0:19:19:728:0:0:0.0,-5.71957,-65.9032 | |
| 12 990235135 . A T 162.285 . SAP=59.4686;EPP=59.4686;SRR=323;DPB=1846.0;MQMR=60.0;DP=1846;PAO=0.0;RPP=59.4686;RPR=26.0;PAIRED=0.0;ODDS=0.902717;MEANALT=1.0;MQM=60.0;SAF=0;PAIREDR=0.0;EPPR=1463.85;SAR=26;NS=447;RPL=0.0;technology.ILLUMINA=1.0;RO=1815;AC=3;AB=0.439024;SRF=1492;AF=0.0033557;GTI=7;AO=26;AN=894;ABP=4.33437;SRP=1637.97;DPRA=2.45;RPPR=3587.87;PQA=0.0;QR=69596;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=771;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:8:8:316:0:0:0.0,-2.40824,-28.835 0/0:6:6:194:0:0:0.0,-1.80618,-17.7833 ./. ./. ./. 0/0:7:7:232:0:0:0.0,-2.10721,-21.2114 ./. 0/0:1:1:29:0:0:0.0,-0.30103,-2.9 0/0:8:8:311:0:0:0.0,-2.40824,-28.3788 0/0:19:19:715:0:0:0.0,-5.71957,-64.7263 | |
| 12 1000235173 . G A 34.1044 . SAP=12.0706;EPP=65.983;SRR=2202;DPB=3855.0;MQMR=60.0;DP=3855;PAO=0.0;RPP=12.0706;RPR=20.0;PAIRED=0.0;ODDS=0.744872;MEANALT=1.0;MQM=60.0;SAF=9;PAIREDR=0.0;EPPR=6789.72;SAR=20;NS=565;RPL=9.0;technology.ILLUMINA=1.0;RO=3826;AC=10;AB=0.0;SRF=1624;AF=0.00884956;GTI=5;AO=29;AN=1130;ABP=0.0;SRP=192.622;DPRA=0.728947;RPPR=510.926;PQA=0.0;QR=135210;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=984;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:19:19:633:0:0:0.0,-5.71957,-57.3032 0/0:7:7:255:0:0:0.0,-2.10721,-23.3143 0/0:3:3:88:0:0:0.0,-0.90309,-8.21333 0/0:5:5:182:0:0:0.0,-1.50515,-16.744 0/0:8:8:250:0:0:0.0,-2.40824,-22.8125 0/0:9:9:305:0:0:0.0,-2.70927,-27.7889 0/0:1:1:36:0:0:0.0,-0.30103,-3.6 0/0:4:4:142:0:0:0.0,-1.20412,-13.135 0/0:11:11:379:0:0:0.0,-3.31133,-34.4545 0/0:25:25:821:0:0:0.0,-7.52575,-74.2184 | |
| 12 1010235183 . G A 111.843 . SAP=4.09604;EPP=20.3821;SRR=2249;DPB=3617.0;MQMR=60.0;DP=3617;PAO=0.0;RPP=4.09604;RPR=5.0;PAIRED=0.0;ODDS=7.68903;MEANALT=1.0;MQM=60.0;SAF=3;PAIREDR=0.0;EPPR=789.078;SAR=5;NS=563;RPL=3.0;technology.ILLUMINA=1.0;RO=3609;AC=2;AB=1.0;SRF=1360;AF=0.0017762;GTI=2;AO=8;AN=1126;ABP=20.3821;SRP=478.533;DPRA=0.621779;RPPR=847.908;PQA=0.0;QR=130048;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=288;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:15:15:518:0:0:0.0,-4.51545,-46.9653 0/0:7:7:268:0:0:0.0,-2.10721,-24.5029 0/0:4:4:138:0:0:0.0,-1.20412,-12.765 0/0:5:5:200:0:0:0.0,-1.50515,-18.4 0/0:9:9:317:0:0:0.0,-2.70927,-28.8822 0/0:9:9:315:0:0:0.0,-2.70927,-28.7 0/0:1:1:37:0:0:0.0,-0.30103,-3.7 0/0:4:4:154:0:0:0.0,-1.20412,-14.245 0/0:8:8:279:0:0:0.0,-2.40824,-25.4588 0/0:13:13:450:0:0:0.0,-3.91339,-40.8462 | |
| 12 1020235223 . G A 14537.4 . SAP=737.234;EPP=737.234;SRR=1733;DPB=2472.0;MQMR=60.0;DP=2472;PAO=0.0;RPP=1403.61;RPR=0.0;PAIRED=0.0;ODDS=2.81255;MEANALT=1.0;MQM=60.0;SAF=89;PAIREDR=0.0;EPPR=3195.82;SAR=556;NS=536;RPL=645.0;technology.ILLUMINA=1.0;RO=1827;AC=194;AB=0.0;SRF=94;AF=0.18097;GTI=1;AO=645;AN=1072;ABP=0.0;SRP=3195.82;DPRA=1.59113;RPPR=3970.29;PQA=0.0;QR=70928;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=24970;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:11:11:423:0:0:0.0,-3.31133,-38.4545 0/0:8:8:307:0:0:0.0,-2.40824,-28.0138 0/0:4:4:146:0:0:0.0,-1.20412,-13.505 0/0:5:5:193:0:0:0.0,-1.50515,-17.756 0/0:11:11:405:0:0:0.0,-3.31133,-36.8182 0/0:6:6:230:0:0:0.0,-1.80618,-21.0833 0/0:2:2:64:0:0:0.0,-0.60206,-6.08 0/0:4:4:143:0:0:0.0,-1.20412,-13.2275 0/0:4:4:162:0:0:0.0,-1.20412,-14.985 0/0:7:7:270:0:0:0.0,-2.10721,-24.6857 | |
| 12 1030235230 . C A 60.0775 . SAP=26.8965;EPP=26.8965;SRR=2;DPB=848.0;MQMR=60.0;DP=848;PAO=0.0;RPP=26.8965;RPR=0.0;PAIRED=0.0;ODDS=1.45025;MEANALT=1.0;MQM=60.0;SAF=11;PAIREDR=0.0;EPPR=1820.53;SAR=0;NS=377;RPL=11.0;technology.ILLUMINA=1.0;RO=837;AC=3;AB=0.625;SRF=835;AF=0.00397878;GTI=2;AO=11;AN=754;ABP=5.18177;SRP=1803.2;DPRA=2.02229;RPPR=1803.2;PQA=0.0;QR=31997;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=355;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. 0/0:2:2:74:0:0:0.0,-0.60206,-7.03 0/0:4:4:162:0:0:0.0,-1.20412,-14.985 0/0:4:4:146:0:0:0.0,-1.20412,-13.505 0/0:1:1:40:0:0:0.0,-0.30103,-4.0 ./. ./. ./. | |
| 12 1040235382 . C T 8629.41 . SAP=1040.97;EPP=1040.97;SRR=0;DPB=2278.0;MQMR=60.0;DP=2278;PAO=0.0;RPP=1040.97;RPR=478.0;PAIRED=0.0;ODDS=1.11213;MEANALT=1.0;MQM=60.0;SAF=478;PAIREDR=0.0;EPPR=3911.66;SAR=0;NS=519;RPL=0.0;technology.ILLUMINA=1.0;RO=1800;AC=180;AB=0.0;SRF=1800;AF=0.17341;GTI=1;AO=478;AN=1038;ABP=0.0;SRP=3911.66;DPRA=1.26917;RPPR=3911.66;PQA=0.0;QR=70392;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=18733;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:9:9:360:0:0:0.0,-2.70927,-32.8 0/0:5:5:195:0:0:0.0,-1.50515,-17.94 0/0:6:6:235:0:0:0.0,-1.80618,-21.5417 0/0:1:1:40:0:0:0.0,-0.30103,-4.0 0/0:16:16:609:0:0:0.0,-4.81648,-55.1906 0/0:6:6:222:0:0:0.0,-1.80618,-20.35 0/0:1:1:40:0:0:0.0,-0.30103,-4.0 0/0:18:18:688:0:0:0.0,-5.41854,-62.3022 ./. 0/0:8:8:318:0:0:0.0,-2.40824,-29.0175 | |
| 12 1050235475 . C G 8117.05 . SAP=888.971;EPP=888.971;SRR=1677;DPB=2086.0;MQMR=60.0;DP=2086;PAO=0.0;RPP=888.971;RPR=0.0;PAIRED=0.0;ODDS=0.350965;MEANALT=1.0;MQM=60.0;SAF=0;PAIREDR=0.0;EPPR=3584.02;SAR=408;NS=525;RPL=408.0;technology.ILLUMINA=1.0;RO=1677;AC=113;AB=0.985782;SRF=0;AF=0.107619;GTI=70;AO=408;AN=1050;ABP=435.504;SRP=3644.57;DPRA=1.16756;RPPR=3584.02;PQA=0.0;QR=65883;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=16249;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL 0/0:17:17:676:0:0:0.0,-5.11751,-61.2376 0/0:13:13:501:0:0:0.0,-3.91339,-45.4754 0/0:6:6:225:0:0:0.0,-1.80618,-20.625 0/0:18:18:669:0:0:0.0,-5.41854,-60.5817 0/0:6:6:237:0:0:0.0,-1.80618,-21.725 0/0:9:9:333:0:0:0.0,-2.70927,-30.34 0/0:6:6:231:0:0:0.0,-1.80618,-21.175 0/0:20:20:738:0:0:0.0,-6.0206,-66.789 0/0:11:11:376:0:0:0.0,-3.31133,-34.1818 0/0:4:4:127:0:0:0.0,-1.20412,-11.7475 | |
| 12 1060240521 . G T 203.196 . SAP=42.0968;EPP=42.0968;SRR=6;DPB=24.0;MQMR=37.6667;DP=24;PAO=0.0;RPP=42.0968;RPR=18.0;PAIRED=0.0;ODDS=20.7343;MEANALT=1.0;MQM=33.8889;SAF=0;PAIREDR=0.0;EPPR=16.0391;SAR=18;NS=19;RPL=0.0;technology.ILLUMINA=1.0;RO=6;AC=38;AB=0.0;SRF=0;AF=1.0;GTI=0;AO=18;AN=38;ABP=0.0;SRP=16.0391;DPRA=1.38462;RPPR=16.0391;PQA=0.0;QR=196;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=522;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. | |
| 12 1070240615 . C A 378.781 . SAP=39.9253;EPP=39.9253;SRR=0;DPB=17.0;MQMR=0.0;DP=17;PAO=0.0;RPP=39.9253;RPR=0.0;PAIRED=0.0;ODDS=9.27203;MEANALT=1.0;MQM=33.8824;SAF=17;PAIREDR=0.0;EPPR=0.0;SAR=0;NS=16;RPL=17.0;technology.ILLUMINA=1.0;RO=0;AC=32;AB=0.0;SRF=0;AF=1.0;GTI=0;AO=17;AN=32;ABP=0.0;SRP=0.0;DPRA=0.0;RPPR=0.0;PQA=0.0;QR=0;RUN=1;CIGAR=1X;LEN=1;NUMALT=1;QA=535;PQR=0.0;TYPE=snp;PRO=0.0 GT:DP:RO:QR:AO:QA:GL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. |
As suggested by jmarshall, The CSI index format support coordinates up to 231. If I index VCF with:
$ ./tabix --csi moved.vcf.gz
Now I can query the VCF correctly:
$ ./tabix moved.vcf.gz 12 | tail -2 | cut -f 1-7
12 1060240521 . G T 203.196 .
12 1070240615 . C A 378.781 .
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
htslib can't deal with positions above ~500000000. Those cases are very common in plants.
Download the latest htslib from github. Compile code, then download
moved.vcffrom gist. Inspect last vcf lines withtail:Now pack the file with bgzip and index it with tabix:
Finally, query the VCF using tabix and chrom
12:All lines after 109 (POS
530164817) were lost.