Reads are marked as full of mismatches in IGV, but cigar string shows full length match

Question

[jsuzuki]

I've posted a screen shot of the IGV alignment of paired end reads and picked out an individual read, pulling up the stats for that read pair. The read that I clicked on is the read directly above the popup window, it is blue and marked with multiple mismatches, places where the read does not match the genome. My question is this: When I look on IGV, that read shows many mismatches, but the cigar shows 150M and 149M, indicating no mismatches in either read pair? Can anybody explain what's going on?

Thank you!

Answer 1

[swbarnes2]

CIGAR strings do not indicate SNPs, only indels and clipping.

[LChart]

To piggyback: "M" in the cigar string indicates an alignment match. You can look at the "NM:" tag for the number of mismatches which, in this case, is 15.

[jsuzuki]

Very helpful addition, thank you both!