CIGAR (Compact Idiosyncratic Gapped Alignment Report)

Defines the sequence of matches/mismatches and deletions (or gaps). The cigar line defines the sequence of matches/mismatches and deletions (or gaps). For example, this cigar line 2MD3M2D2M will mean that the alignment contains 2 matches/mismatches, 1 deletion (number 1 is omitted in order to save some space), 3 matches/mismatches, 2 deletions and 2 matches/mismatches. If the original sequence is:

Original sequence: AACGCTT

The aligned sequence will be:
cigar line: 2MD3M2D2M M M D M M M D D M M
A A - C G C - - T T

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