I'm a little confused with my output from bowtie (not bowtie2) and hoping someone may be able to clarify stuff for me. For my bowtie command I selected no mismatches using the flag
-v 0. However, when I look at the output, many alignments in my sam file have
XM:i:3 i.e. 3 mismatches in the alignment.
If anyone could please explain why the alignments have mismatches if I selected no mismatches in the command line it would be a great help!