Mismatches In Bowtie

Question

[roll]

Hi,

I am trying to understand bowtie mismatch option -v I have this sequence of 16bp and I try to match it in the whole genome. First i tried -v 0 and then -v 1 With -v 1 i would expect that there would be 1 mismatch in the output. But when i looked at the output of bowtie (column5) it all seems the same - no mismatch. So what is actually happening? Am i looking at the wrong column?

Best,

Answer 1

[Bharat Iyengar]

-v option is for maximum allowed mismatch.

If there is a better match, it will be reported.

If you specify --best --strata option, then only the best alignments will be reported.

[roll]

Thank you. That is great