Hi everyone,
I have checked the tophat sam file from tophat1.0.11, and found one reads have been reported twice(same genome location but different optional fields). Why two different mismatch( NM:i:0 , NM:i:1) number for the same reads and same mapping location?
HWI-EAS244_1_1_61_293_716_0_1_6480169;1 19 chr1 1231272 255 47M76N28M = 1231188 0 ACTTCTTTTCCACGTATTTGTCCTTGATCCAGGCCTCCTTGTCCTGCCGGGAGCTGCTGGCTGTGGGTTTCCTGC P\MMY]LR\`a]a``^[FWa`]a[aa\^`a`a^\``X`X```]ZZa\V\aaaaaaa__aa_ababbabbbbaab` NM:i:0 XS:A:- NS:i:0
HWI-EAS244_1_1_61_293_716_0_1_6480169;1 19 chr1 1231272 255 47M76N28M = 1231188 0 ACTTCTTTTCCACGTATTTGTCCTTGATCCAGGCCTCCTTGTCCTGCCGGGAGCTGCTGGCTGTGGGTTTCCTGC P\MMY]LR\`a]a``^[FWa`]a[aa\^`a`a^\``X`X```]ZZa\V\aaaaaaa__aa_ababbabbbbaab` NM:i:1 XS:A:- NS:i:0
I have checked the tophat sam file from tophat1.0.11, and found one reads have been reported twice(same genome location but different optional fields). Why two different mismatch( NM:i:0 , NM:i:1) number for the same reads and same mapping location?
HWI-EAS244_1_1_61_293_716_0_1_6480169;1 19 chr1 1231272 255 47M76N28M = 1231188 0 ACTTCTTTTCCACGTATTTGTCCTTGATCCAGGCCTCCTTGTCCTGCCGGGAGCTGCTGGCTGTGGGTTTCCTGC P\MMY]LR\`a]a``^[FWa`]a[aa\^`a`a^\``X`X```]ZZa\V\aaaaaaa__aa_ababbabbbbaab` NM:i:0 XS:A:- NS:i:0
HWI-EAS244_1_1_61_293_716_0_1_6480169;1 19 chr1 1231272 255 47M76N28M = 1231188 0 ACTTCTTTTCCACGTATTTGTCCTTGATCCAGGCCTCCTTGTCCTGCCGGGAGCTGCTGGCTGTGGGTTTCCTGC P\MMY]LR\`a]a``^[FWa`]a[aa\^`a`a^\``X`X```]ZZa\V\aaaaaaa__aa_ababbabbbbaab` NM:i:1 XS:A:- NS:i:0
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