Hello everyone,

I was using the Isaac aligner for analyze the human sample. When I view the results of bam files from the Isaac v4, I see the unmapped reads.

I'm wondering which criteria or values (i.e., the number of mismatches in the read, base quality, mapping quality ...etc) decide to reads as unmapped reads? I think there is no mismatch percentage cutoff for mapped reads.

I would appreciate a lot if you could help me out.