Mercurial > repos > urgi-team > vcfgandalftools
comparison test-data/VCFFiltering_DP_4_200_output.vcf @ 0:3552a8d9f51c draft
Uploaded
| author | urgi-team |
|---|---|
| date | Tue, 10 Nov 2015 08:30:56 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:3552a8d9f51c |
|---|---|
| 1 ##fileformat=VCFv4.1 | |
| 2 ##fileDate=20140725 | |
| 3 ##source=freeBayes v0.9.13-2-ga830efd | |
| 4 ##phasing=none | |
| 5 ##DetectedFormat=freebayes | |
| 6 ##FILTER=<ID=G_AN,Description="The SNP has been filtered ; out of AN range(over 2)"> | |
| 7 ##FILTER=<ID=G_AF,Description="The SNP has been filtered ; out of AF range(under 0.9)"> | |
| 8 ##FILTER=<ID=G_DP,Description="The SNP has been filtered ; out of DP range(4 - 200)"> | |
| 9 ##FILTER=<ID=InDel,Description="The SNP has been filtered ; InDel detected"> | |
| 10 ##FILTER=<ID=Nmatch,Description="The SNP has been filtered ; reference base detected : N"> | |
| 11 ##INFO=<ID=G_AN,Number=1,Type=Integer,Description="Total number of alleles calculated by VCFFiltering"> | |
| 12 ##INFO=<ID=G_AF,Number=1,Type=Float,Description="frequency of the most supported alternative allele calculated by VCFFiltering"> | |
| 13 ##INFO=<ID=G_base,Number=1,Type=String,Description="base of the most supported alternative allele found by VCFFiltering"> | |
| 14 ##INFO=<ID=G_DP,Number=1,Type=Integer,Description="total depth calculated by VCFFiltering"> | |
| 15 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> | |
| 16 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> | |
| 17 ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> | |
| 18 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> | |
| 19 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | |
| 20 ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> | |
| 21 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> | |
| 22 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> | |
| 23 ##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> | |
| 24 ##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> | |
| 25 ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> | |
| 26 ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> | |
| 27 ##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> | |
| 28 ##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> | |
| 29 ##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> | |
| 30 ##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> | |
| 31 ##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> | |
| 32 ##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> | |
| 33 ##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"> | |
| 34 ##INFO=<ID=SAP,Number=A,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"> | |
| 35 ##INFO=<ID=AB,Number=A,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"> | |
| 36 ##INFO=<ID=ABP,Number=A,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"> | |
| 37 ##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> | |
| 38 ##INFO=<ID=RPP,Number=A,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"> | |
| 39 ##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"> | |
| 40 ##INFO=<ID=EPP,Number=A,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"> | |
| 41 ##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"> | |
| 42 ##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> | |
| 43 ##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> | |
| 44 ##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> | |
| 45 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> | |
| 46 ##INFO=<ID=CIGAR,Number=A,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."> | |
| 47 ##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> | |
| 48 ##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> | |
| 49 ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> | |
| 50 ##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> | |
| 51 ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> | |
| 52 ##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> | |
| 53 ##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> | |
| 54 ##INFO=<ID=technology.illumina,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from illumina"> | |
| 55 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| 56 ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> | |
| 57 ##FORMAT=<ID=GL,Number=G,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"> | |
| 58 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> | |
| 59 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> | |
| 60 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> | |
| 61 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> | |
| 62 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> | |
| 63 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G15_myco | |
| 64 chr_1 235 . C T 21.392 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=0.865778;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=35;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:77:-4.63556,0,-2.351 | |
| 65 chr_1 244 . C T 21.1881 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=0.865718;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=35;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:76:-4.61503,0,-2.35102 | |
| 66 chr_1 253 . T C 73.475 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=34;MQMR=0;NS=1;NUMALT=1;ODDS=7.23646;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-8.62509,-0.841726,0 | |
| 67 chr_1 333 . G A 24.2337 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=3.07477;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=82;QR=24;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:24:2:82:-4.69685,0,-1.39164 | |
| 68 chr_1 354 . G A 20.5104 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=2.23682;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=28;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:28:2:78:-4.66174,0,-1.75556 | |
| 69 chr_1 363 . G A 40.3032 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36;MQMR=0;NS=1;NUMALT=1;ODDS=5.91856;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:63:-5.23324,-0.570398,0 | |
| 70 chr_1 1531 . G A 73.2764 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=0;NS=1;NUMALT=1;ODDS=7.23732;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=115;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:115:-9.08235,-0.842098,0 | |
| 71 chr_1 1565 . A G 14.5726 G_AF AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=38;MQMR=35;NS=1;NUMALT=1;ODDS=3.30493;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=71;RO=2;RPP=7.35324;RPPR=3.0103;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.50;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 0/1:4:2:71:2:71:-5.0654,0,-4.84835 | |
| 72 chr_1 1589 . A G 102.964 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36.5;MQMR=0;NS=1;NUMALT=1;ODDS=8.55461;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=155;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:155:-10,-1.11316,0 | |
| 73 chr_1 1635 . G A 95.7333 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=38.5;MQMR=0;NS=1;NUMALT=1;ODDS=8.55365;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=141;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:141:-10,-1.11274,0 | |
| 74 chr_1 2624 . C T 122.967 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=44.75;MQMR=0;NS=1;NUMALT=1;ODDS=8.5553;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=156;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:156:-10,-1.11346,0 | |
| 75 chr_1 2670 . C T 30.7231 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.739044;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:41:2:71:-5.60946,0,-2.40604 | |
| 76 chr_1 2671 . G A 30.0349 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.738983;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:41:2:70:-5.5406,0,-2.40606 | |
| 77 chr_1 2686 . A G 28.1218 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.861385;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=39;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:3:1:39:2:67:-5.31237,0,-2.3529 | |
| 78 chr_1 2697 . G A 66.8365 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23789;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=104;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:104:-9.39261,-0.842345,0 | |
| 79 chr_1 2699 . G A 75.6507 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23781;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=103;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:103:-9.31979,-0.842311,0 | |
| 80 chr_1 2747 . C T 52.6764 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=5.92179;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=81;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:81:-7.07265,-0.5718,0 | |
| 81 chr_1 3616 . C T 96.527 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=8.55506;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=153;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:153:-10,-1.11336,0 | |
| 82 chr_1 3624 . A G 99.7577 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=8.55532;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=158;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:158:-10,-1.11347,0 | |
| 83 chr_1 3630 . G A 119.888 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=13.8677;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=9.87182;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=191;QR=0;RO=0;RPP=13.8677;RPPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:191:-10,-1.38419,0 | |
| 84 chr_1 3657 . T C 146.729 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=9.87224;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=204;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:204:-10,-1.38437,0 | |
| 85 chr_1 3681 . C T 141.607 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=8.80089;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.5;MQMR=0;NS=1;NUMALT=1;ODDS=11.1867;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=201;QR=0;RO=0;RPP=8.80089;RPPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:201:-10,-1.65422,0 | |
| 86 chr_1 3746 . G A 143.027 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=42.8;MQMR=0;NS=1;NUMALT=1;ODDS=9.87133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=177;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:177:-10,-1.38398,0 | |
| 87 chr_1 3766 . TGG TG 207.378 InDel AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1M1D1M;DP=7;DPB=4.66667;DPRA=0;EPP=3.32051;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.8571;MQMR=0;NS=1;NUMALT=1;ODDS=12.5052;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=267;QR=0;RO=0;RPP=3.32051;RPPR=0;RUN=1;SAF=1;SAP=10.7656;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=del;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=7;G_Base=TG GT:DP:RO:QR:AO:QA:GL 1/1:7:0:0:7:267:-10,-1.9258,0 | |
| 88 chr_1 3804 . C T 168.638 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=42.1667;MQMR=0;NS=1;NUMALT=1;ODDS=11.188;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=213;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=1;SAP=8.80089;SAR=5;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:213:-10,-1.65476,0 | |
| 89 chr_1 3845 . G A 130.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=6.91895;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.8;MQMR=0;NS=1;NUMALT=1;ODDS=9.87163;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=184;QR=0;RO=0;RPP=13.8677;RPPR=0;RUN=1;SAF=1;SAP=6.91895;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:184:-10,-1.38411,0 | |
| 90 chr_1 3857 . G A 72.7109 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23836;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=113;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:113:-9.98004,-0.84255,0 | |
| 91 chr_1 4299 . C T 48.7928 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=48;NS=1;NUMALT=1;ODDS=2.04069;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=100;QR=34;RO=1;RPP=9.52472;RPPR=5.18177;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.75;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:1:34:3:100:-7.69498,0,-2.01683 | |
| 92 chr_1 4311 . A G 138.174 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=6.91895;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40.2;MQMR=0;NS=1;NUMALT=1;ODDS=9.8711;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=179;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=3;SAP=3.44459;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:179:-10,-1.38387,0 | |
| 93 chr_1 4357 . C T 141.385 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40.2;MQMR=0;NS=1;NUMALT=1;ODDS=9.87061;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=181;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:181:-10,-1.38366,0 | |
| 94 chr_1 4372 . C T 57.8383 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=48;NS=1;NUMALT=1;ODDS=0.86483;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=40;RO=1;RPP=3.73412;RPPR=5.18177;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.75;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:1:40:3:110:-8.53351,0,-2.5275 | |
| 95 chr_1 4389 . C T 176.339 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.80219;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=45.4286;MQMR=48;NS=1;NUMALT=1;ODDS=6.11702;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=247;QR=37;RO=1;RPP=3.32051;RPPR=5.18177;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.88;G_DP=8;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:8:1:37:7:247:-10,0,-1.14959 | |
| 96 chr_1 4398 . T C 197.868 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.80219;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=45.4286;MQMR=0;NS=1;NUMALT=1;ODDS=12.5039;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=243;QR=0;RO=0;RPP=3.32051;RPPR=0;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=7;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:7:0:0:7:243:-10,-1.92523,0 | |
| 97 chr_1 4404 . T C 168.543 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=46.3333;MQMR=0;NS=1;NUMALT=1;ODDS=11.1873;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=209;QR=0;RO=0;RPP=4.45795;RPPR=0;RUN=1;SAF=2;SAP=4.45795;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:209:-10,-1.65448,0 | |
| 98 chr_1 4475 . C T 81.0612 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=47;MQMR=0;NS=1;NUMALT=1;ODDS=7.2379;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-9.86084,-0.842352,0 | |
| 99 chr_1 4540 . C T 72.5101 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23698;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=101;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:101:-9.00573,-0.841952,0 | |
| 100 chr_1 4580 . C T 81.3345 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23817;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=119;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:119:-9.88816,-0.842465,0 | |
| 101 chr_1 4611 . C G 51.9857 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.5;MQMR=0;NS=1;NUMALT=1;ODDS=5.92133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=69;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:69:-6.40152,-0.5716,0 | |
| 102 chr_1 4661 . A G 19.7502 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=43;NS=1;NUMALT=1;ODDS=0.834078;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=35;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:76:-5.08162,0,-2.36476 | |
| 103 chr_1 4678 . G A 21.951 G_AF;G_DP AB=0.666667;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=43;NS=1;NUMALT=1;ODDS=0.136458;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 0/1:3:1:41:2:68:-4.94794,0,-2.78626 | |
| 104 chr_1 4686 . C T 81.6957 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23731;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-9.44717,-0.842096,0 | |
| 105 chr_1 4699 . G A 103.379 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36.75;MQMR=0;NS=1;NUMALT=1;ODDS=8.55324;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=140;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:140:-10,-1.11256,0 | |
| 106 chr_1 4717 . C T 18.6085 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=34;NS=1;NUMALT=1;ODDS=1.12012;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=40;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:40:2:66:-4.87583,0,-2.24054 | |
| 107 chr_1 4727 . G A 43.4619 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=32;MQMR=0;NS=1;NUMALT=1;ODDS=5.91984;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:66:-5.54913,-0.570955,0 | |
| 108 chr_1 4747 . C T 40.3421 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=34;MQMR=0;NS=1;NUMALT=1;ODDS=5.92045;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:68:-5.83919,-0.571218,0 | |
| 109 chr_1 3305168 . T A,G 280.615 G_AF AB=0.75,0.25;ABP=9.52472,9.52472;AC=1,1;AF=0.5,0.5;AN=2;AO=9,3;CIGAR=1X,1X;DP=12;DPB=12;DPRA=0,0;EPP=9.04217,3.73412;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=4.632;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=319,107;QR=0;RO=0;RPP=9.04217,9.52472;RPPR=0;RUN=1,1;SAF=4,2;SAP=3.25157,3.73412;SAR=5,1;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;technology.illumina=1,1;G_AN=2;G_AF=0.75;G_DP=12;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/2:12:0:0:9,3:319,107:-10,-8.89435,-6.43456,-10,0,-10 | |
| 110 chr_1 3305169 . T A,G 280.615 G_AF AB=0.25,0.75;ABP=9.52472,9.52472;AC=1,1;AF=0.5,0.5;AN=2;AO=9,3;CIGAR=1X,1X;DP=12;DPB=12;DPRA=0,0;EPP=9.04217,3.73412;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=4.632;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=319,107;QR=0;RO=0;RPP=9.04217,9.52472;RPPR=0;RUN=1,1;SAF=4,2;SAP=3.25157,3.73412;SAR=5,1;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;technology.illumina=1,1;G_AN=2;G_AF=0.75;G_DP=12;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/2:12:0:0:9,3:319,107:-10,-8.89435,-6.43456,-10,0,-10 |