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Old 06-08-2017, 10:04 AM   #10
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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Bacteria have circular genomes, represented in fasta files as linear with a breakpoint somewhere. Mapping (and thus coverage calculation) is less accurate at the ends due to the artificial break; BBMap will place a read spanning the break on either the left end or the right end, but not both. You might want to look at the ends to see if the uncovered bases are there.
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