bowtie mismatch 0 alignment output

0

Hello there!

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!

Thanks


sequencing


bam


sam


bowtie


rna-seq

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