CompGenWS/finch_740027.vcf at master · eacooper400/CompGenWS · GitHub

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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
JH740027	39010	.	T	C	8903.59	.	.	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JH740027	438619	.	T	G	2016.98	.	.	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JH740027	602243	.	C	G	3072.24	.	.	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JH740027	618095	.	TCA	CCA,CCG	9570.31	.	.	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JH740027	1371706	.	G	C,A	416.78	.	.	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JH740027	1677211	.	A	G	4936.14	.	.	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JH740027	1677221	.	G	A	4631.28	.	.	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JH740027	1740625	.	G	A	1970.04	.	.	GT:DP:GL:QA:RO:AO:QR:GQ	0/0:13:0,-3.91339,-42.2077:0:13:0:465:48.9694	0/1:11:-25.5512,0,-8.89282:292:3:8:107:99	0/0:8:0,-2.40824,-23.1775:0:8:0:254:33.9179	0/0:6:0,-1.80618,-19.9833:0:6:0:218:27.8973	0/0:4:0,-1.20412,-12.95:0:4:0:140:21.8767	0/1:14:-28.5159,0,-16.015:323:5:9:184:99	.:.:.:.:.:.:.:.	0/0:6:0,-1.80618,-19.8:0:6:0:216:27.8973	0/0:8:0,-2.40824,-24.7288:0:8:0:271:33.9179	0/0:4:0,-1.20412,-11.7475:0:4:0:127:21.8767	0/1:14:-16.843,0,-28.607:193:9:5:324:99	0/1:17:-29.2438,0,-25.2745:329:8:9:285:99	0/0:20:0,-6.0206,-65.884:0:20:0:728:70.0415	0/0:16:0,-4.81648,-51.475:0:16:0:568:58.0003	0/0:13:0,-3.91339,-41.4815:0:13:0:457:48.9694	0/0:9:0,-2.70927,-26.7867:0:9:0:294:36.9282	0/0:7:0,-2.10721,-22.3086:0:7:0:244:30.9076	0/0:14:0,-4.21442,-44.7221:0:14:0:493:51.9797	0/0:5:0,-1.50515,-15.64:0:5:0:170:24.887	0/1:19:-2.49843,0,-46.4275:63:17:2:551:16.9291	0/0:5:0,-1.50515,-14.628:0:5:0:159:24.887	0/1:11:-23.9087,0,-7.67949:274:3:8:94:99	0/0:6:0,-1.80618,-20.5333:0:6:0:224:27.8973	0/1:11:-9.54615,0,-24.7299:114:8:3:283:81.9797	0/1:5:-9.94818,0,-6.71485:112:2:3:76:85.9922	0/0:14:0,-4.21442,-44.8129:0:14:0:494:51.9797	1/1:9:-29.4289,-2.70927,0:323:0:9:0:0.0138034	0/0:6:0,-1.80618,-19.6167:0:6:0:214:27.8973	0/0:11:0,-3.31133,-36.9091:0:11:0:406:42.9488	0/1:8:-13.3119,0,-12.4794:150:4:4:141:99	0/1:26:-1.7151,0,-72.353:74:24:2:859:7.91632	0/0:13:0,-3.91339,-41.9354:0:13:0:462:48.9694	0/1:12:-16.4904,0,-22.8749:187:7:5:258:99	0/0:4:0,-1.20412,-12.8575:0:4:0:139:21.8767	0/1:18:-39.5435,0,-18.9251:448:6:12:219:99	0/1:13:-36.7131,0,-1.30055:435:1:12:41:62.8681	0/0:16:0,-4.81648,-52.7438:0:16:0:582:58.0003	0/0:9:0,-2.70927,-30.5222:0:9:0:335:36.9282	0/0:10:0,-3.0103,-32.305:0:10:0:355:39.9385	0/1:4:-6.79403,0,-6.31903:76:2:2:71:58.7056	0/0:15:0,-4.51545,-43.7013:0:15:0:482:54.99	0/0:7:0,-2.10721,-21.8514:0:7:0:239:30.9076	0/0:15:0,-4.51545,-43.1573:0:15:0:476:54.99	0/0:6:0,-1.80618,-17.05:0:6:0:186:27.8973	0/1:18:-47.4505,0,-7.85315:551:3:15:111:99	0/1:10:-12.9094,0,-18.3786:147:6:4:208:99	0/0:14:0,-4.21442,-45.6293:0:14:0:503:51.9797	0/0:12:0,-3.61236,-39.3308:0:12:0:433:45.9591	0/0:23:0,-6.92369,-76.5078:0:23:0:846:79.0723	0/0:13:0,-3.91339,-42.2985:0:13:0:466:48.9694	0/1:29:-20.0463,0,-68.1085:247:22:7:781:99	0/0:13:0,-3.91339,-43.66:0:13:0:481:48.9694	0/0:14:0,-4.21442,-46.5364:0:14:0:513:51.9797	0/0:11:0,-3.31133,-35.6364:0:11:0:392:42.9488	0/0:11:0,-3.31133,-35.7273:0:11:0:393:42.9488	0/0:8:0,-2.40824,-26.1888:0:8:0:287:42.8042	0/0:4:0,-1.20412,-14.245:0:4:0:154:30.763	0/1:9:-13.3586,0,-16.0431:151:5:4:181:99	0/0:24:0,-7.22472,-78.3913:0:24:0:867:90.9688	0/0:14:0,-4.21442,-45.1757:0:14:0:498:60.866	0/1:11:-17.595,0,-14.7173:199:5:6:167:99	0/1:12:-5.42718,0,-30.4212:76:10:2:354:36.3185	0/0:11:0,-3.31133,-33:0:11:0:363:51.8351	0/0:3:0,-0.90309,-9.14667:0:3:0:98:27.7527	0/0:18:0,-5.41854,-57.1406:0:18:0:631:72.9072	0/1:13:-12.1684,0,-27.732:143:9:4:316:99	1/1:7:-21.12,-2.10721,0:231:0:7:0:0.228593	0/1:3:-5.93903,0,-3.07403:67:1:2:35:31.5346	0/1:17:-8.355,0,-42.2557:114:14:3:491:70.5586	0/0:6:0,-1.80618,-17.6:0:6:0:192:36.7836	1/1:4:-12.58,-1.20412,0:136:0:4:0:0.0279247	0/0:6:0,-1.80618,-19.7083:0:6:0:215:36.7836	0/0:7:0,-2.10721,-20.2057:0:7:0:221:39.7939	0/1:3:-6.60403,0,-3.37403:74:1:2:38:47.9988	0/0:14:0,-4.21442,-45.8107:0:14:0:505:60.866	.:.:.:.:.:.:.:.	.:.:.:.:.:.:.:.	.:.:.:.:.:.:.:.	.:.:.:.:.:.:.:.	.:.:.:.:.:.:.:.	.:.:.:.:.:.:.:.	.:.:.:.:.:.:.:.	.:.:.:.:.:.:.:.	.:.:.:.:.:.:.:.	.:.:.:.:.:.:.:.	.:.:.:.:.:.:.:.	.:.:.:.:.:.:.:.	0/0:3:0,-0.90309,-10.36:0:3:0:111:46.4065	0/0:7:0,-2.10721,-22.4:0:7:0:245:58.4477	0/0:19:0,-5.71957,-61.2863:0:19:0:677:94.5711	0/0:11:0,-3.31133,-36.5455:0:11:0:402:70.4889	0/1:15:-15.5221,0,-31.4491:180:10:5:357:90.7711	0/0:28:0,-8.42884,-89.9054:0:28:0:995:99	0/1:21:-3.31559,0,-56.8343:77:19:2:672:2.29912	0/0:20:0,-6.0206,-65.16:0:20:0:720:97.5815	1/1:19:-64.4898,-5.71957,0:713:0:19:0:43.8567	0/0:8:0,-2.40824,-27.7168:0:8:0:304:26.3287	1/1:10:-33.8264,-3.0103,0:372:0:10:0:16.764	1/1:8:-28.2585,-2.40824,0:310:0:8:0:10.7434	0/1:9:-11.7062,0,-14.9393:156:5:4:192:99	0/1:8:-15.605,0,-8.13005:196:3:5:113:99	0/0:13:0,-3.91339,-45.523:0:13:0:502:41.3802	0/0:13:0,-3.91339,-44.7995:0:13:0:494:41.3802	0/0:8:0,-2.40824,-25.717:0:8:0:282:26.3287	0/0:8:0,-2.40824,-27.5338:0:8:0:302:26.3287	0/0:13:0,-3.91339,-45.523:0:13:0:502:41.3802	0/0:4:0,-1.20412,-13.7714:0:4:0:149:14.2875	0/0:11:0,-3.31133,-37.3346:0:11:0:411:35.3596	0/0:5:0,-1.50515,-17.9228:0:5:0:195:17.2978	0/0:2:0,-0.60206,-6.7419:0:2:0:71:1.78533	0/0:9:0,-2.70927,-29.2292:0:9:0:321:29.339	0/0:4:0,-1.20412,-13.9559:0:4:0:151:14.2875	0/0:12:0,-3.61236,-39.397:0:12:0:434:38.3699	0/0:4:0,-1.20412,-13.2202:0:4:0:143:14.2875	0/0:11:0,-3.31133,-37.6949:0:11:0:415:35.3596	0/0:6:0,-1.80618,-20.519:0:6:0:224:20.3081