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Old 07-23-2012, 08:07 AM   #1
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Location: Dallas

Join Date: Dec 2011
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Default SAM alignment result: match without reference report


I used novoalign to map some sequence and got this kind of result in SAM format:

SRR2002 0 * 175710298 0 23M13H * 0 0 CAATTGTCAGAGGTGAAATTCTT B>7<?99@:9<=:;569=>B@=@ PG:Z:novoalign AS:i:55 UQ:i:55 NM:i:2 MD:Z:15G0C6

It is mapped to the genome, with the match start, strand, even the mismatches are reported. However, the third column, where should be "chrN" turned out to be a star.

Any one encountered this situation? Could any body kindly tell me why this happened?

Thanks in advance!
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