If a read overlaps a region perfectly except for a single masked base pair position, does bowtie consider that position a mismatch in the read? Or does bowtie ignore that position, and consider it a perfect alignment?
I'm thinking about aligning to a reference genome that is hard-masked to SNPs, and I'm wondering if this will cause fewer reads to align due to more mismatches.
How long are your reads?
The reads are 50 base pairs.