vg giraffe to get the
GAF file. I have some questions about the 12th column, that is mapping quality(MAPQ). The difference of
MAPQ standard between aligners makes me confused.
I found MAPQ is in the range[0, 60] which similar with
bwa-mem, but I don not find a good explanation.Through reading some questions in vg github, I only know low
MAPQ means reads multimapped and
MAPQ 60 means reads aligned very well. And I found the
MAPQ of unmapped reads is also 0.
MAPQ only reflect whether reads map to multiple locations? How about base mismatch? How can I get the unique mapping?
Could someone kindly provide an explanation? I would greatly appreciate anyone who can assist me with this.