BWA produces odd alignment results

[dandyrilla]

I tried to get a uniquely mapped reads from BWA alignment, so I filtering out the alignments without XT:A:U in SAM line.

However, BWA produces odd aligned reads, which is both unmapped and uniquely mapped.

These reads below have both SAM flag which means 'reads unmapped' and mapping position.(chrom, pos)

How can that be? Have you ever gotten such reads?

SRR101341.21640516 4 chr3 199501827 0 33M * 0 0 GACCCTAACCCTAACCCTAACCCTAACCCTAAC 0)@@)?''0-68?09384;<5=)A;56@>167: XT:A:U NM:i:0 XN:i:1 X0:i:1 X1:i:557 XM:i:0 XO:i:0 XG:i:0 MD:Z:33

SRR101344.29575296 133 chr11 134452345 15 43M chr12 92723370 0 TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGAGG CCCCCCCCCCCCCCCCCCDCCCCCDCCCCCBB@CCCBCCCC@C XT:A:U NM:i:0 XN:i:3 SM:i:15 AM:i:0 X0:i:1 X1:i:6 XM:i:0 XO:i:0 XG:i:0 MD:Z:43 XA:Z:chr3,+199385175,43M,1;chrX,+154913557,43M,1;chrY,+57772757,43M,1;chr11,+134452000,43M,1;chr1,-397,43M,1;chr18,-25,43M,1;

thanks (^______^)

[swbarnes2]

bwa concatenates reference sequences together, and if a read hangs off of one reference, and onto another, bwa will both give it a mapping position, and a 4 flag.

More commonly, sam specs call for the unmapped read of a pair to be given the mapping position of its mapped mate, and the 4 flag.

But from your coordinates, I'm betting that the first is the answer.

[dandyrilla]

Why 'XT:A:U' is in the unmapped line?

Thanks, swbarnes2!

And then,
why 'XT:A:U' is in the unmapped line?

I know that 'XT:A:U' means uniquely mapped read.
Is it right?
What does it mean?