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finch_740035.vcf
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finch_740035.vcf
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##fileformat=VCFv4.2
##commandline="/Users/lizcooper/programs/freebayes/bin/freebayes -f /Volumes/LC_WD/Geospiza_UCSC/geoFor1.fa -F 0.2 -q 30 -m 20 --min-coverage 10 --no-indels --genotype-qualities Fortis_merged.bam"
##commandline="/Users/lizcooper/programs/freebayes/bin/freebayes -f /Volumes/LC_WD/Geospiza_UCSC/geoFor1.fa -F 0.2 -q 30 --min-coverage 5 --no-indels --genotype-qualities Fuliginosa_sorted.bam"
##fileDate=20151013
##commandline="/Users/lizcooper/programs/freebayes/bin/freebayes -f /Volumes/LC_WD/Geospiza_UCSC/geoFor1.fa -F 0.2 -q 30 --min-coverage 5 --no-indels --genotype-qualities Magnirostris_sorted.bam"
##fileDate=20151013
##source=freeBayes v0.9.20-16-g3e35e72
##reference=/Volumes/LC_WD/Geospiza_UCSC/geoFor1.fa
##commandline="/Users/lizcooper/programs/freebayes/bin/freebayes -f /Volumes/LC_WD/Geospiza_UCSC/geoFor1.fa -F 0.2 -q 30 --min-coverage 5 --no-indels --genotype-qualities Scandens_sorted.bam"
##fileDate=20150626
##source=freeBayes v0.9.20-18-gc054850-dirty
##reference=/panicle/liz/Reference_Genomes/geoFor1.fa
##phasing=none
##commandline="/panicle/wpoehlm/freebayes/bin/freebayes -f /panicle/liz/Reference_Genomes/geoFor1.fa -F 0.2 -m 50 -q 30 --min-coverage 20 --no-indels --genotype-qualities /panicle/transfer/Finch2015_merged.bam"
##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=AF,Number=A,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=A,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=A,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=A,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=A,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=A,Type=Integer,Description="Number of alternate observations on the forward strand">
##INFO=<ID=SAR,Number=A,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=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">
##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">
##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">
##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
##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">
##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=A,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=A,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=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">
##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=A,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=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
##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.">
##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
##INFO=<ID=MQM,Number=A,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=A,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.F1.bam,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from F1.bam">
##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=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">
##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=A,Type=Integer,Description="Alternate allele observation count">
##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
##source_20151014.1=vcf-merge(r940) ../Fortis_BAM/Fortis_merged.vcf.gz ../Fuliginosa_BAM/Fuliginosa_merged.vcf.gz ../Magnirostris_BAM/Magnirostris_merged.vcf.gz ../Scandens_BAM/Scandens_merge.vcf.gz Finch2015_allScaff.vcf.gz
##sourceFiles_20151014.1=0:../Fortis_BAM/Fortis_merged.vcf.gz,1:../Fuliginosa_BAM/Fuliginosa_merged.vcf.gz,2:../Magnirostris_BAM/Magnirostris_merged.vcf.gz,3:../Scandens_BAM/Scandens_merge.vcf.gz,4:Finch2015_allScaff.vcf.gz
##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT FO3687 FO3895 FO3658 FO3676 FO3754 FO3914 FO3934 FO3636 FO3631 FO3774 FO3697 FO3633 FO3894 FO3738 FO3747 FO3790 FO3681 FO3652 FO3755 FO3642 FO3959 FO3699 FO851 FO3752 FO3753 FO3640 FO824 FO520 FO3923 FO855 FO3943 FO3670 FO3913 FO3844 FO3960 FO3661 FO3162 FO3695 FO3171 FO3751 FO3835 FO367 FO3048 FO3582 FO241 FO3657 FO687 FO3748 FO3922 FO3402 FO3924 FO3539 FO3683 FO3750 FO3574 FU303 FU295 FU278 FU359 FU342 FU290 FU393 FU475 FU293 FU262 FU348 FU512 FU411 FU286 FU261 FU506 FU343 FU306 FU309 FU294 MA3607 MA3690 MA3688 MA3684 MA3626 MA3746 MA3666 MA3693 MA3656 MA3665 MA3740 MA3810 SC3565 SC3583 SC3587 SC3610 SC3647 SC3653 SC3655 SC3664 FOM1 FOM2 FUS1 FUS2 FUZ1 FUZ2 MAG1 MAG2 MAG3 MAG4 MAG5 SCM1 SCM2 L.noctisB1 L.noctisB2 L.noctisB3 L.noctisB4 L.noctisB5 T.bicolorB1 T.bicolorB2 T.bicolorB3
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JH740035 1531993 . TTGATGGT CTGACAGC 3813.62 . . GT:GQ:AO:QR:RO:GL:QA:DP 1/1:27.2428:2:0:0:-7.315,-0.60206,0:77:2 1/1:42.2943:7:0:0:-24.1371,-2.10721,0:264:7 0/1:13.7059:4:38:1:-13.3463,0,-2.99382:153:5 1/1:27.2428:2:0:0:-7.6,-0.60206,0:80:2 1/1:30.2531:3:0:0:-11.1067,-0.90309,0:119:3 0/1:40.9214:3:74:2:-10.3215,0,-6.52485:116:5 .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. 1/1:39.284:6:0:0:-20.8083,-1.80618,0:227:6 1/1:42.2943:7:0:0:-23.5886,-2.10721,0:258:7 1/1:24.2325:1:0:0:-4.1,-0.30103,0:41:1 1/1:39.284:6:0:0:-21.45,-1.80618,0:234:6 1/1:30.2531:3:0:0:-10.92,-0.90309,0:117:3 1/1:42.2943:7:0:0:-24.96,-2.10721,0:273:7 1/1:30.2531:3:0:0:-11.0133,-0.90309,0:118:3 0/1:59.2598:10:118:3:-32.9975,0,-9.15798:383:14 .:.:.:.:.:.:.:. 1/1:42.2943:7:0:0:-25.3257,-2.10721,0:277:7 0/0:2.65426e-06:0:39:1:0,-0.30103,-3.9:0:1 0/1:56.1972:13:117:3:-42.5902,0,-8.85171:492:16 0/1:99:6:315:8:-20.9881,0,-28.0069:237:14 1/1:42.2943:7:0:0:-23.8629,-2.10721,0:261:7 1/1:48.3149:9:0:0:-29.8844,-2.70927,0:328:9 1/1:30.2531:3:0:0:-10.2667,-0.90309,0:110:3 0/1:14.4874:5:41:1:-16.728,0,-3.07197:193:6 1/1:33.2634:4:0:0:-13.9675,-1.20412,0:151:4 0/0:2.65426e-06:0:40:1:0,-0.30103,-4:0:1 1/1:24.2325:1:0:0:-3.4,-0.30103,0:34:1 1/1:36.2737:5:0:0:-17.756,-1.50515,0:193:5 1/1:27.2428:2:0:0:-6.555,-0.60206,0:69:2 0/1:10.1466:6:39:1:-19.1796,0,-2.63789:223:7 1/1:30.2531:3:0:0:-11.2,-0.90309,0:120:3 0/1:17.7471:3:40:1:-10.5046,0,-3.39794:119:4 1/1:33.2634:4:0:0:-14.06,-1.20412,0:152:4 1/1:30.2531:3:0:0:-10.1733,-0.90309,0:109:3 1/1:39.284:6:0:0:-21.32,-1.80618,0:236:7 0/1:12.508:2:33:1:-7.17403,0,-2.87403:80:3 0/1:15.7059:4:40:1:-13.3463,0,-3.19382:153:5 1/1:24.2325:1:0:0:-4,-0.30103,0:40:1 .:.:.:.:.:.:.:. 1/1:48.3149:9:0:0:-30.6133,-2.70927,0:336:9 0/1:42.5221:4:77:2:-13.8924,0,-6.68491:157:6 0/1:97.0775:5:155:4:-17.1471,0,-13.7286:193:9 0/1:1.07103:8:40:1:-26.35,0,-2.24497:308:9 0/1:69.382:4:115:3:-13.1269,0,-10.1702:148:7 1/1:24.2325:1:0:0:-4,-0.30103,0:40:1 0/1:20.7574:1:40:1:-3.59897,0,-3.69897:39:2 1/1:30.2531:3:0:0:-11.2933,-0.90309,0:121:3 0/1:46.4632:1:79:2:-3.67403,0,-7.07903:41:3 1/1:24.2325:1:0:0:-3.9,-0.30103,0:39:1 0/1:7.14662:6:36:1:-19.6379,0,-2.33789:228:7 1/1:51.3252:10:0:0:-34.944,-3.0103,0:384:10 .:.:.:.:.:.:.:. 0/1:16.7471:3:39:1:-9.75794,0,-3.29794:111:4 1/1:33.2634:4:0:0:-14.1525,-1.20412,0:153:4 1/1:24.2704:1:0:0:-3.9,-0.30103,0:39:1 0/1:10.1622:5:39:1:-17.372,0,-2.87197:200:6 1/1:30.2911:3:0:0:-10.4533,-0.90309,0:112:3 0/1:1.32204:8:40:1:-26.9887,0,-2.24497:315:9 1/1:33.3014:4:0:0:-13.505,-1.20412,0:146:4 1/1:36.3117:5:0:0:-17.848,-1.50515,0:194:5 0/1:7.8214:6:39:1:-20.1879,0,-2.63789:234:7 1/1:48.3529:9:0:0:-30.561,-2.70927,0:339:10 1/1:36.3117:5:0:0:-17.664,-1.50515,0:192:5 1/1:33.3014:4:0:0:-14.5225,-1.20412,0:157:4 0/1:18.432:1:40:1:-3.49897,0,-3.69897:38:2 1/1:27.2808:2:0:0:-7.22,-0.60206,0:76:2 1/1:30.2911:3:0:0:-10.4533,-0.90309,0:112:3 1/1:39.322:6:0:0:-19.9833,-1.80618,0:218:6 0/1:73.6902:3:120:3:-9.85485,0,-10.6949:111:6 0/1:13.3807:4:40:1:-13.4388,0,-3.19382:154:5 1/1:27.2808:2:0:0:-6.935,-0.60206,0:73:2 0/1:70.8895:3:117:3:-9.48152,0,-10.4149:107:6 .:.:.:.:.:.:.:. 0/1:11.1622:5:40:1:-15.716,0,-2.97197:182:6 0/0:0.0178195:0:40:1:0,-0.30103,-4:0:1 0/1:26.5484:6:74:2:-20.1223,0,-6.06892:230:8 .:.:.:.:.:.:.:. 1/1:23.2901:3:0:0:-10.7333,-0.90309,0:115:3 .:.:.:.:.:.:.:. 1/1:17.2695:1:0:0:-4.1,-0.30103,0:41:1 1/1:17.2694:1:0:0:-3.4,-0.30103,0:34:1 1/1:17.2695:1:0:0:-4,-0.30103,0:40:1 1/1:32.321:6:0:0:-20.4417,-1.80618,0:223:6 1/1:23.2901:3:0:0:-10.08,-0.90309,0:108:3 1/1:20.2798:2:0:0:-7.6,-0.60206,0:80:2 0/1:14.4096:2:41:1:-7.07903,0,-3.67403:79:3 .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:. .:.:.:.:.:.:.:.
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