Question About Samtools Flag Number 117

Question

[Alby]

One of the rows in my alignment data has the samtool flag of 117.

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

to figure out what it means. The following is the summary for flag 117:

1. read paired
2. read unmapped
3. read reverse strand
4. mate reverse strand
5. first in pair

My question is, how could a read be "unmapped" and be "reverse strand(aligned to reference)" at the same time? My guess is samtools define "unmapped" as anything that is not "properly mapped"(meaning both reads in a pair mapped correctly)?

Thanks

[Arun]

just to clarify, what do you mean by samtool flag? The flag is definitely ambiguous. In any case, as long as the flag "read unmapped" is set, I wouldn't consider it for any downstream analysis.

Answer 1

[Vikas Bansal]

You can find an answer by Istvan here.

117: read paired, read unmapped, read on reverse strand, mate on reverse strand, first in pair

So the output is correct, what it probably means is that the read and its mate are both on the reverse strand therefore the mapping of this read (and its mate) are questionable, thus it got the unmapped designation.

[lelle]

I am not sure if this is correct. The SAM specification states: "If 0x4 is set, no assumptions can be made about [...] bits 0x2, 0x10 and 0x100 ..." where 0x10 is reverse complement 0x20 mate is reverse complement. So to me this means if 0x4 is set the others can be random. Never the less the explanation Istvan came up with might be right, but I would not rely on it.