Reads are marked as full of mismatches in IGV, but cigar string shows full length match
1
0
Entering edit mode
15 months ago
jsuzuki ▴ 10

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?

enter image description here

Thank you!

cigar IGV • 914 views
ADD COMMENT
4
Entering edit mode
15 months ago

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

ADD COMMENT
2
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Very helpful addition, thank you both!

ADD REPLY

Login before adding your answer.

Traffic: 1588 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6