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Old 02-08-2017, 05:59 PM   #3
Brian Bushnell
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Location: Walnut Creek, CA

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Additionally, lengths and coverage are important here. Possibly, 99% of the bases map to the 27 contigs that match the reference, and the other contigs are short, degenerate contigs from errors or chimerism. Or maybe you're assembling various adapter sequences (another form of chimerism, in a way). It depends on how you're doing the alignment and assembly, and what kind of data you have. Can you describe the situation in more detail? Also, have you BLASTed the unaligned sequences, or compared them to known adapter sequences?
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