Mercurial > repos > iuc > bbtools_bbmerge

comparison test-data/cv_output.vcf @ 0:fc029a9b4d07 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
author iuc
date Mon, 06 Feb 2023 18:06:47 +0000
parents
children cab19c0452c4
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-1:000000000000 0:fc029a9b4d07
1 ##fileformat=VCFv4.2
2 ##BBMapVersion=
3 ##ploidy=2
4 ##rarity=1.00000
5 ##minallelefraction=0.10000
6 ##reads=2207
7 ##pairedReads=0
8 ##properlyPairedReads=0
9 ##readLengthAvg=
10 ##properPairRate=0.00000
11 ##totalQualityAvg=
12 ##mapqAvg=43.348
13 ##reference=
14 ##contig=<ID=NC_002945.4,length=7000>
15 ##FILTER=<ID=FAIL,Description="Fail">
16 ##FILTER=<ID=PASS,Description="Pass">
17 ##INFO=<ID=SN,Number=1,Type=Integer,Description="Scaffold Number">
18 ##INFO=<ID=STA,Number=1,Type=Integer,Description="Start">
19 ##INFO=<ID=STO,Number=1,Type=Integer,Description="Stop">
20 ##INFO=<ID=TYP,Number=1,Type=String,Description="Type">
21 ##INFO=<ID=R1P,Number=1,Type=Integer,Description="Read1 Plus Count">
22 ##INFO=<ID=R1M,Number=1,Type=Integer,Description="Read1 Minus Count">
23 ##INFO=<ID=R2P,Number=1,Type=Integer,Description="Read2 Plus Count">
24 ##INFO=<ID=R2M,Number=1,Type=Integer,Description="Read2 Minus Count">
25 ##INFO=<ID=AD,Number=1,Type=Integer,Description="Allele Depth">
26 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
27 ##INFO=<ID=MCOV,Number=1,Type=Integer,Description="Minus Coverage">
28 ##INFO=<ID=PPC,Number=1,Type=Integer,Description="Paired Count">
29 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Fraction">
30 ##INFO=<ID=RAF,Number=1,Type=Float,Description="Revised Allele Fraction">
31 ##INFO=<ID=LS,Number=1,Type=Integer,Description="Length Sum">
32 ##INFO=<ID=MQS,Number=1,Type=Integer,Description="MAPQ Sum">
33 ##INFO=<ID=MQM,Number=1,Type=Integer,Description="MAPQ Max">
34 ##INFO=<ID=BQS,Number=1,Type=Integer,Description="Base Quality Sum">
35 ##INFO=<ID=BQM,Number=1,Type=Integer,Description="Base Quality Max">
36 ##INFO=<ID=EDS,Number=1,Type=Integer,Description="End Distance Sum">
37 ##INFO=<ID=EDM,Number=1,Type=Integer,Description="End Distance Max">
38 ##INFO=<ID=IDS,Number=1,Type=Integer,Description="Identity Sum">
39 ##INFO=<ID=IDM,Number=1,Type=Integer,Description="Identity Max">
40 ##INFO=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count">
41 ##INFO=<ID=FLG,Number=1,Type=Integer,Description="Flagged">
42 ##INFO=<ID=CED,Number=1,Type=Integer,Description="Contig End Distance">
43 ##INFO=<ID=HMP,Number=1,Type=Integer,Description="Homopolymer Count">
44 ##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
45 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Ref+, Ref-, Alt+, Alt-">
46 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
47 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
48 ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allele Depth">
49 ##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele Fraction">
50 ##FORMAT=<ID=RAF,Number=1,Type=Float,Description="Revised Allele Fraction">
51 ##FORMAT=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count">
52 ##FORMAT=<ID=FLG,Number=1,Type=Integer,Description="Flagged">
53 ##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
54 ##FORMAT=<ID=SC,Number=1,Type=Float,Description="Score">
55 ##FORMAT=<ID=PF,Number=1,Type=String,Description="Pass Filter">
56 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
57 NC_002945.4 976327 . N T 22.21 PASS SN=0;STA=976326;STO=976327;TYP=SUB;R1P=2;R1M=0;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=77;MQM=40;BQS=48;BQM=24;EDS=111;EDM=65;IDS=1930;IDM=972;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1.0000:1.0000:0:0:0.9980:22.21:PASS
58 NC_002945.4 1501932 . N C 27.20 PASS SN=0;STA=1501931;STO=1501932;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=88;MQM=44;BQS=64;BQM=39;EDS=74;EDM=38;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1.0000:1.0000:0:0:0.9980:27.20:PASS
59 NC_002945.4 3380579 . N G 27.85 PASS SN=0;STA=3380578;STO=3380579;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=289;MQS=87;MQM=44;BQS=75;BQM=38;EDS=105;EDM=63;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1.0000:1.0000:0:0:0.9980:27.85:PASS
60 NC_002945.4 3646293 . N A 23.34 PASS SN=0;STA=3646292;STO=3646293;TYP=SUB;R1P=1;R1M=1;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=291;MQS=86;MQM=44;BQS=76;BQM=38;EDS=44;EDM=31;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=1.0000 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1.0000:1.0000:0:0:1.0000:23.34:PASS