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Old 06-08-2017, 04:43 AM   #7
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,080

Did you inspect the alignment using IGV or a genome browser of some kind? It should be reasonably clear what those numbers mean. Looks like you have a small fraction of the genome (0.15%) that does not have at least one read covering it.

Differences like this could be due to your strain being slightly different than the reference sequence.
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