idxstats non mapped reads

Question

[vmicrobio]

Hi,

I'm doing alignment using bwa, trying to determine if sequences are mapped or not to a reference. I tried to compare fastq files to one reference and obtained my output in csv using samtools idxstats. I got this output:

AE005174.2  5528445 2080495 6121
*   0   0   92628

and do not understand what is the difference between non mapped reads 6121 and 92628. I read samtools documentation and answers on forums but it's still not clear for me. Usually I do it using numerous references and got always 0 instead of 6121.

Thanks for your clarifications!

Answer 1

[Devon Ryan]

The 6121 reads are mates of reads that map to AE005174.2. The reads on * are those where neither mate of a pair maps. In general, reads are assigned to the coordinate of their mate if they aren't mapped but their mate is.

[vmicrobio]

that's pretty clear, thanks!