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!
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written
by
vmicrobio
1 answer
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.
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