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
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
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