My question is about the CIGAR specification.
The documentation states:
M 0 alignment match (can be a sequence match or mismatch)
I 1 insertion to the reference
Q1: If I have a CIGAR string
99M170661N26M, does that mean I have 99 matches. Can that also mean 99 mismatches? What about 98 matches and 1 mismatch? The specification states it could be a sequence match or mismatch.
Q2: Assuming I'm doing an RNA-seq experiment. In my CIGAR string
99M170661N26M, does that mean my read aligns to an intron which has 17066 bases? Can I think like: "I have a spliced read which aligns to two exons and an intron. I have 99 matches to my first exon and 26 matches to my second exon. I have 17066 matches to my intron."?
Can I get the number of matches in my read? Does that even make sense? For example, how do I know if I have 10 exact matches?