Mercurial > repos > iuc > bbtools_bbmap

comparison test-data/cv_output.vcf @ 9:83d0df824438 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
author iuc
date Tue, 27 Aug 2024 10:13:16 +0000
parents ce6000f3e457
children
comparison
equal deleted inserted replaced
8:33262f7b3e23 9:83d0df824438
1 ##fileformat=VCFv4.2 1 ##fileformat=VCFv4.2
2 ##BBMapVersion= 2 ##BBMapVersion=39.08
3 ##ploidy=2 3 ##ploidy=2
4 ##rarity=1.00000 4 ##rarity=1.00000
5 ##minallelefraction=0.10000 5 ##minallelefraction=0.10000
6 ##reads=2207 6 ##reads=2207
7 ##pairedReads=0 7 ##pairedReads=0
8 ##properlyPairedReads=0 8 ##properlyPairedReads=0
9 ##readLengthAvg= 9 ##readLengthAvg=145.462
10 ##properPairRate=0.00000 10 ##properPairRate=0.00000
11 ##totalQualityAvg= 11 ##totalQualityAvg=36.580
12 ##mapqAvg=43.348 12 ##mapqAvg=43.348
13 ##reference= 13 ##reference=/home/bag/projects/code/tools-iuc/tools/bbtools/test-data/NC_002945v4.fasta
14 ##contig=<ID=NC_002945.4,length=7000> 14 ##contig=<ID=NC_002945.4,length=7000>
15 ##FILTER=<ID=FAIL,Description="Fail"> 15 ##FILTER=<ID=FAIL,Description="Fail">
16 ##FILTER=<ID=PASS,Description="Pass"> 16 ##FILTER=<ID=PASS,Description="Pass">
17 ##INFO=<ID=SN,Number=1,Type=Integer,Description="Scaffold Number"> 17 ##INFO=<ID=SN,Number=1,Type=Integer,Description="Scaffold Number">
18 ##INFO=<ID=STA,Number=1,Type=Integer,Description="Start"> 18 ##INFO=<ID=STA,Number=1,Type=Integer,Description="Start">
51 ##FORMAT=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count"> 51 ##FORMAT=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count">
52 ##FORMAT=<ID=FLG,Number=1,Type=Integer,Description="Flagged"> 52 ##FORMAT=<ID=FLG,Number=1,Type=Integer,Description="Flagged">
53 ##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias"> 53 ##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
54 ##FORMAT=<ID=SC,Number=1,Type=Float,Description="Score"> 54 ##FORMAT=<ID=SC,Number=1,Type=Float,Description="Score">
55 ##FORMAT=<ID=PF,Number=1,Type=String,Description="Pass Filter"> 55 ##FORMAT=<ID=PF,Number=1,Type=String,Description="Pass Filter">
56 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 56 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT dataset_4f1db038-76fe-46bc-a222-dfc4894a8ff2.dat
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 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;RAF=1;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 1/1:2:2:1:1:0:0:0.9980:22.21: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 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;RAF=1;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 1/1:2:2:1:1:0:0:0.9980:27.20: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 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;RAF=1;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 1/1:2:2:1:1:0:0:0.9980:27.85: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 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;RAF=1;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 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1:1:0:0:1:23.34:PASS