Question about sam flags.

Question

[mangfu100]

Hi there.

While I am studying the samtools flags, I saw site below and thought that it was very useful.

https://ppotato.wordpress.com/2010/08/25/samtool-bitwise-flag-paired-reads/

However, In this webpages, I can't figure out that why samtools flags 81,161,97,145,65,129,113,188 is wrong insert size?

I looked this site up several times, but I didn't understand why all these samtools flags refer to wrong insert size.

Can you help me?

Answer 1

[John Marshall]

These flag values have both ends mapped, but not properly paired. The properly-paired/aligned flag is described as

each segment properly aligned according to the aligner

which is not enormously clear, but typically means that the reads are mapped with appropriate orientation and insert size such that they plausibly reflect the whole template having been "nicely" mapped as a whole to the reference.

So having both ends mapped but not properly paired means that they have been mapped with either implausible orientations or an implausible insert size.

Answer 2

[GouthamAtla]

Better refer this site for sam file flag information, which is also claimed to be source for the PDF:

http://broadinstitute.github.io/picard/explain-flags.html