Editing Sequence alignment (section)

===CIGAR Format===
Ref.  :        GTCGTAGAATA <br />
[[Read (biology)|Read]]:             CACGTAG—TA <br />
CIGAR: 2S5M2D2M
where: <br />
2S = 2 soft clipping (could be mismatches, or a read longer than the matched sequence) <br />
5M = 5 matches or mismatches <br />
2D = 2 deletions <br />
2M = 2 matches or mismatches

The original CIGAR format from the [https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate exonerate alignment program] did not distinguish between mismatches or matches with the M character.

The SAMv1 spec document defines newer CIGAR codes.  In most cases it is preferred to use the '=' and 'X' characters to denote matches or mismatches rather than the older 'M' character, which is ambiguous.

{| class="wikitable"
! CIGAR Code
! BAM Integer
! Description
! Consumes query
! Consumes reference
|-
| M||0||alignment match (can be a sequence match or mismatch)||yes||yes
|-
| I||1||insertion to the reference||yes||no
|-
| D||2||deletion from the reference||no||yes
|-
| N||3||skipped region from the reference||no||yes
|-
| S||4||soft clipping (clipped sequences present in SEQ)||yes||no
|-
| H||5||hard clipping (clipped sequences NOT present in SEQ)||no||no
|-
| P||6||padding (silent deletion from padded reference)||no||no
|-
| =||7||sequence match||yes||yes
|-
| X||8||sequence mismatch||yes||yes
|-
|
|}
* "Consumes query" and "consumes reference" indicate whether the CIGAR operation causes the alignment to step along the query sequence and the reference sequence respectively.
* H can only be present as the first and/or last operation.
* S may only have H operations between them and the ends of the CIGAR string.
* For mRNA-to-genome alignment, an N operation represents an intron. For other types of alignments, the interpretation of N is not defined.
* Sum of lengths of the M/I/S/=/X operations shall equal the length of SEQ