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.
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written
by
debanjan.roy12 •
1 answer
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=
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