Hi,

I'm not sure if its a bug with the bowtie's sam output, but all my mapping quality would take the value of 255 while the bit flag would take on values of either 0,4,16. I had run bowtie in colorspace.

Has anyone else encountered a similar issue?

Here's a sample of the sam output with the qwerky values.

1279_33_430_F3 4 * 0 0 * * 0 0 TGGTGACCTGGGCCCTGAGGANCGCGTTGATCTACCTCCGCTCAATTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XM:i:0

1279_33_409_F3 16 chr6 49186545 255 50M * 0 0 TATTCGTACTGAAAATCAAGATCAAGCGAGCTTTTGCCCTTCTGCTCCAC Iqqqqqqqqqqqqqqqqqqqqqqqqqq!Iq!!qqqqqqqqqqqqqqqqqI XA:i:2 MD:Z:50 NM:i:0 CM:i:2

1279_34_783_F3 0 chr16 11144009 255 50M * 0 0 TATGTGCTTGGCTGAGGAGCCAATGGGGCGAAGCTACCATCTGTGGGATT Iqqqqqqqqqqqqqqqqqqqq!Iqqqqqqqqqqqqqqqqqqqqqqq!!qI XA:i:2 MD:Z:50 NM:i:0 CM:i:2

1279_40_121_F3 0 chr17 39983712 255 50M * 0 0 ACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACC Iqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq!!qqq!!qqqqI XA:i:2 MD:Z:50 NM:i:0 CM:i:2

1279_41_567_F3 16 chr6 49186546 255 50M * 0 0 ATTCGTACTGAAAATCAAGATCAAGCGAGCTTTTGCCCTTCTGCTCCACG IqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqI XA:i:0 MD:Z:50 NM:i:0 CM:i:0

-burt

I'm not sure if its a bug with the bowtie's sam output, but all my mapping quality would take the value of 255 while the bit flag would take on values of either 0,4,16. I had run bowtie in colorspace.

Has anyone else encountered a similar issue?

Here's a sample of the sam output with the qwerky values.

1279_33_430_F3 4 * 0 0 * * 0 0 TGGTGACCTGGGCCCTGAGGANCGCGTTGATCTACCTCCGCTCAATTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XM:i:0

1279_33_409_F3 16 chr6 49186545 255 50M * 0 0 TATTCGTACTGAAAATCAAGATCAAGCGAGCTTTTGCCCTTCTGCTCCAC Iqqqqqqqqqqqqqqqqqqqqqqqqqq!Iq!!qqqqqqqqqqqqqqqqqI XA:i:2 MD:Z:50 NM:i:0 CM:i:2

1279_34_783_F3 0 chr16 11144009 255 50M * 0 0 TATGTGCTTGGCTGAGGAGCCAATGGGGCGAAGCTACCATCTGTGGGATT Iqqqqqqqqqqqqqqqqqqqq!Iqqqqqqqqqqqqqqqqqqqqqqq!!qI XA:i:2 MD:Z:50 NM:i:0 CM:i:2

1279_40_121_F3 0 chr17 39983712 255 50M * 0 0 ACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACC Iqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq!!qqq!!qqqqI XA:i:2 MD:Z:50 NM:i:0 CM:i:2

1279_41_567_F3 16 chr6 49186546 255 50M * 0 0 ATTCGTACTGAAAATCAAGATCAAGCGAGCTTTTGCCCTTCTGCTCCACG IqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqI XA:i:0 MD:Z:50 NM:i:0 CM:i:0

-burt

## Comment