Mercurial > repos > jpayne > snp_pipeline

comparison test-data/samples/sample1/reads.sam @ 58:d53281e6edae

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planemo upload
author jpayne
date Mon, 17 Jun 2024 02:57:10 -0400
parents eefdd97a6749
children
comparison
equal deleted inserted replaced
57:d3095ad12f24 58:d53281e6edae
1 @HD VN:1.0 SO:unsorted 1 @HD VN:1.0 SO:unsorted
2 @SQ SN:gi|9626243|ref|NC_001416.1| LN:48502 2 @SQ SN:gi|9626243|ref|NC_001416.1| LN:48502
3 @PG ID:bowtie2 PN:bowtie2 VN:2.3.3.1 CL:"/usr/local/bin/bowtie2-align-s --wrapper basic-0 --reorder -X 1000 -p 2 -x reference/lambda_virus -1 samples/sample1/sample1_1.fastq -2 samples/sample1/sample1_2.fastq" 3 @PG ID:bowtie2 PN:bowtie2 VN:2.3.5.1 CL:"/home/chet/miniconda3/envs/mulled-v1-3aaacfa732fb5a9a4edb89d75dc27c600fe12abcc61b59ef7e28f09be834e1ba/bin/bowtie2-align-s --wrapper basic-0 -q -x ./reference -p 1 --reorder -X 1000 -1 ./forward.gz -2 ./reverse.gz"
4 r1 83 gi|9626243|ref|NC_001416.1| 16266 42 97M = 16003 -360 GCAATACAGCGGTATCTGGGACGGAACGTTTAAACCGGCATACAGCAACAACATGGCCTGGCGTCTGTGGGATTTGCTGACCCATCCGCGCTACGGC *5:441C0)"E,A%72$9-"1%A:8%-0<80-;6H8%7643HB>9*;8BED.D#.2?44:4'5)0<6F6F1*C71A.D;G0G<2<9.6/B:3")?4' AS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:61T11A23 YS:i:0 YT:Z:CP 4 r1 83 gi|9626243|ref|NC_001416.1| 16266 42 97M = 16003 -360 GCAATACAGCGGTATCTGGGACGGAACGTTTAAACCGGCATACAGCAACAACATGGCCTGGCGTCTGTGGGATTTGCTGACCCATCCGCGCTACGGC *5:441C0)"E,A%72$9-"1%A:8%-0<80-;6H8%7643HB>9*;8BED.D#.2?44:4'5)0<6F6F1*C71A.D;G0G<2<9.6/B:3")?4' AS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:61T11A23 YS:i:0 YT:Z:CP
5 r1 163 gi|9626243|ref|NC_001416.1| 16003 42 58M = 16266 360 GTGGTGATGGGTAACCTGCCGCCGCGCCCGTTTAATATCCGGATGCGCAGGATGACGC );A!/,6B:8=(*2GE1FGA>0/,?>),%.,/3+@D(C=<53!$H"HE-$79*HD?4< AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:58 YS:i:-6 YT:Z:CP 5 r1 163 gi|9626243|ref|NC_001416.1| 16003 42 58M = 16266 360 GTGGTGATGGGTAACCTGCCGCCGCGCCCGTTTAATATCCGGATGCGCAGGATGACGC );A!/,6B:8=(*2GE1FGA>0/,?>),%.,/3+@D(C=<53!$H"HE-$79*HD?4< AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:58 YS:i:-6 YT:Z:CP
6 r2 83 gi|9626243|ref|NC_001416.1| 35315 42 60M = 35108 -267 CCTGTTTCTCTGCGNGACGTTCGCGGCGGCGTNTTTGTGCATCCATCTGGATTCTCCTGT E*CD88'0F(71,0A>GA4:@@+CB%@/8369*H2%!"0CE/BE<:4F)3&1BF&:*7#2 AS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14C17G27 YS:i:-6 YT:Z:CP 6 r2 83 gi|9626243|ref|NC_001416.1| 35315 42 60M = 35108 -267 CCTGTTTCTCTGCGNGACGTTCGCGGCGGCGTNTTTGTGCATCCATCTGGATTCTCCTGT E*CD88'0F(71,0A>GA4:@@+CB%@/8369*H2%!"0CE/BE<:4F)3&1BF&:*7#2 AS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14C17G27 YS:i:-6 YT:Z:CP
7 r2 163 gi|9626243|ref|NC_001416.1| 35108 42 112M = 35315 267 TGCTGTACCATGTGCGCTGATTCTTGCGCTCAATACGTTGAAGGTTGCTTTCAANCTGTTTGTGGTATTCAGCCAGCACTGTAAGGTCTATCGGATTTAGTGCGCTTTCTAC F*E;2#!93)*446F)3<FF#((G6B<E#D,4@=.-@<@/E59H,$1!D%+35#8#)&)9@A?AC%+-*!(C<!5@3+;4F?&A?=/4G#9&91.<,66!=#089'-(;16? AS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:40C13T57 YS:i:-2 YT:Z:CP 7 r2 163 gi|9626243|ref|NC_001416.1| 35108 42 112M = 35315 267 TGCTGTACCATGTGCGCTGATTCTTGCGCTCAATACGTTGAAGGTTGCTTTCAANCTGTTTGTGGTATTCAGCCAGCACTGTAAGGTCTATCGGATTTAGTGCGCTTTCTAC F*E;2#!93)*446F)3<FF#((G6B<E#D,4@=.-@<@/E59H,$1!D%+35#8#)&)9@A?AC%+-*!(C<!5@3+;4F?&A?=/4G#9&91.<,66!=#089'-(;16? AS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:40C13T57 YS:i:-2 YT:Z:CP
8 r3 99 gi|9626243|ref|NC_001416.1| 31597 42 82M = 31746 319 GAGCCGGAACTTCATGAAATCCCGGGAGGTAAACGGGCATNTCAGTTCAAGGCCGTTGCCGTAACTGCATAAACCATCGGGA 1.,5<.+40387,24@.:42&*2&"5/$H&4@#-E-$D>G)>7@@9!?&"'/6+*8#3:H**C&H7B@+G!(E<",(&"G.* AS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:40T21C19 YS:i:-11 YT:Z:CP 8 r3 99 gi|9626243|ref|NC_001416.1| 31597 42 82M = 31746 319 GAGCCGGAACTTCATGAAATCCCGGGAGGTAAACGGGCATNTCAGTTCAAGGCCGTTGCCGTAACTGCATAAACCATCGGGA 1.,5<.+40387,24@.:42&*2&"5/$H&4@#-E-$D>G)>7@@9!?&"'/6+*8#3:H**C&H7B@+G!(E<",(&"G.* AS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:40T21C19 YS:i:-11 YT:Z:CP