bowtie2 "Pct aligned concordantly >1 times" question

Question

[mark.rose]

Hello

Bowtie2 reports on "Pct aligned concordantly >1 times", does that imply that the multiple concordant alignments map equally well?

Thanks

Answer 1

[Devon Ryan]

Yes, these alignments are only for concordantly aligned pairs that multimap equally well (and concordantly!) to multiple places. These tend to be low complexity regions, in my experience.

[mark.rose]

Thanks a lot. In my case they are not low complexity but multicopy regions