# Why most aligners do not output the "X" CIGAR operation?

As I read the SAM spec, the "X" CIGAR operator represents a mismatch. This seems useful as we can know where are the mismatches without looking at the reference genome. However, many popular aligners such as BWA do not output "X". Why do they omit "X"?

• Strangely enough, the mismatch information is stored in the MD tag (at least for BWA), so it appears to have been a conscious decision rather than a matter of simplicity. Jun 3 '17 at 2:31
• They also generally don't output =. Jun 3 '17 at 9:54
• @DevonRyan I think it will either output M or X/= so if they omit X they will also automatically omit = Aug 30 '17 at 14:48