BWA output bitwise flag for mapped/unmapped reads

[wenhuang]

Hi everybody,

I have a question on a strange alignment I got with BWA (0.5.9). I have come up with a minimal test sequence



@5:84:16665:11131:Y
AGAGAGAACAGAGAACAGAGAACAGAGAACAGAGAACAGAGAACAGAGAACAGAGAACAGAGAAGAGG
+
fdffffff]cffff[aa_]aPVVSYQaa\afc`cffcfffdWf`fadaWd`]aZ^TV]X_TaSWaQ[Z



which apparently can map to the drosophila genome (dm3/R5).

and has the following SAM output




5:84:16665:11131:Y 4 chr2LHet 368806 11 68M * 0 0 AGAGAGAACAGAGAACAGAGAACAGAGAACAGAGAACAGAGAACAGAGAACAGAGAACAGAGAAGAGG GEGGGGGG>DGGGG<BB@>B1774:2BB=BGDADGGDGGGE8GAGBEB8EA>B;?57>9@5B48B2<; XT:A:U NM:i:1 X0:i:1 X1:i:15 XM:i:1 XO:i:0 XG:i:0 MD:Z:1C66




what baffles me is the bitwise flag = 4, which indicates that this read is unmapped.

Anybody has any idea what is happening here?

Thank you,

Wen

[wenhuang]

I think I have found the answer in this post

http://seqanswers.com/forums/showthread.php?t=12767

It turns out the alignment was at the end of the chromosome and contained a overhang which apparently mapped to the next chromosome.