Re: [Samtools-help] quick question : samtools flagstat

[Gmail <apa...@gm...>]

Hey Abhi,

These are the reads that are mapped some where or the other -not necessarily within the Insert size range.
Your ' properly paired ' reads will be a subset of these reads.
They are all flagged for sure.For more info on what a flag could explain I refer to:

http://picard.sourceforge.net/explain-flags.html

Aparna

Sent from my iPhone 4S

On Jun 22, 2012, at 2:32 PM, Abhishek Pratap <abh...@gm...> wrote:

> Hey Guys
> 
> I can't seem to recollect the meaning of one of the lines in the samtools flagstats default output. Could you please clarify
> 
>  15653466 + 0 with itself and mate mapped
> 
> 
> What does "with itself and mate mapped" means. These are not singletons as there is a diff field for that.  Also what is the flag for this ?
> 
> 
> Thanks!
> -Abhi
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