bwa-0.7.12 AS:i and XS:i match but MAPQ = 0

Question

[suzanne.mcgaugh]

Hi,

I was hoping someone might be able to point me to a nice explanation of how the bwa AS:i are determined.

Also, I was hoping that someone might be able to offer an explanation for the sam alignment below. MAPQ = 0, but AS:i:90 and XS:i:90. Does this simply mean that, yes, the read mapped in multiple places, but both had the same alignment score? If that is the case, why is there no XA tag?

It is a single end rad tag.This was mapped with bwa-0.7.12, bwa mem all default parameters except -L 10 to filter some of the soft clipped reads.

1_1101_16130_18632_1_1    0    Scaffold178    1828936    0    90M    *    0    0    AATTCTGCCGTGATTTGGGCAGCCGTGGTTTTATGTTTTTTGGATACAATCCGGGTTAGCACCCGAACATCCCTTTCAGACAGCTTCCTC    B<B<<F<<FFFFFFFFFFBBBF/FFFFFF<BFFBBFFFFFFF/FFF/FFBFFFFFFFB</BFFFFFBFFF/FF<F<FFFBFFFFFFBFFB    NM:i:0    MD:Z:90    AS:i:90    XS:i:90

Thanks very much for any answers.

[Istvan Albert]

as far as I know MAPQ=0 does (or should) indicate multi-mapped reads but then it should also fill in the XA tags. Kind of a head scratcher.