Understanding SAM file format

Question

[KVC_bioinfo]

Hello All,

I am trying to understand the sam output from the alignment. following is example:

[query_name]    16  [Chr_name]  [position]  28  [cigar] *   0   0   [long_seq]  *   NM:i:11017  ms:i:912    AS:i:882    nn:i:0  ts:A:+  tp:A:P  cm:i:170    s1:i:835    s2:i:0

from This link I understand the what the first 11 field means. However, I am unable to understand the fields after 11th fields. Can someone help me understand them?

Thank you in advance.

[lionair]

The fields after 11th field are optional fields. Hope this link helps. It listed all the optional fields specification.

https://samtools.github.io/hts-specs/SAMtags.pdf

Answer 1

[Hussain Ather]

In the link you gave, look at section 1.5 "The alignment section: optional fields." It says

All optional fields follow the TAG:TYPE:VALUE format where TAG is a two-character string that matches /[A-Za-z][A-Za-z0-9]/

And it explains what those tags, types, and values are.