Reconciling bwa XA: field

[nrnoyes]

Hello,

I am in the process of trying to understand bwa output, so excuse this question if it is very naive.

I have used the -n option with sampe in order to output all alternative hits. In several instances, the "best hit" for a read (not sure what to call it since it's not actually the "best") is the same reference sequence as the "alternative hit", although the "best hit" is coded as "XT:A:U" in the XT field. I interpret this as meaning that this read has more than one equally-good hit, but it's still a unique hit, and furthermore the two equally-good hits are the same.

The only way I can explain this is that the read aligns to the same reference sequence, BUT at two "equally-good" locations within the reference sequence.

Can anyone confirm that this is, in fact, the case with these reads?

Thanks very much,

Noelle

[TiborNagy]

A read can not be unique, if it has more than one equally good hits. The -n argument is just set the maximum number of alignments.