In Cigar String, What Is The Difference Between 'M' And 'X'

Question

[debanjan.roy12]

Hello, I am new to exome sequencing analysis. I got 2 variants among which one was confirmed by Sanger Sequencing. It had a general CIGAR string associated with it. ( some matches, then mismatches/insertions/deletions, then again some matches). The other unconfirmed mutation has a good "QUAL" value but has a CIGAR string as "CIGAR=1X". CIGAR documentation tells about M representing an alignment match and X representing a sequence mismatch.

I am unable to understand this and so I would really appreciate any help in understanding this kind of CIGAR representation and what does it tell about that mutation.

Thank you in advance.

Answer 1

[Pierre Lindenbaum]

M means that both READ and REF are aligned. It's the best score for a pairwise alignment. E:g

AAATGGG
||| |||
AAACGGG

cigar string: 7M

M doesn't mean that READ and REF are the same base. You can substitue M by X or =

'=' means REF and READ are the same .

'X' means REF and READ are not the same.

cigar string 3=1X3=