Misinterpretation of TLEN field in SAM output

[Jakob Nissen]

Sorry to spam you here up to the christmas holidays, but:

The TLEN field in the SAM output should be the distance from the leftmost position to the rightmost position within each group of reads, not within a single group of reads. That is, if the forward read maps to pos 41..290, and the reverse read maps to pos 491..740, then the TLEN is (740 - 41 + 1) = 700. More specifically, it is 700 for the forward read and -700 for the reverse read.

It looks like KMA reports the length of the mapped segment only for that particular read in the TLEN field without considering its mate.

Edit: It looks like KMA does not include any mate pair information in the SAM file, like mate mapping template or position at all.