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Old 01-03-2018, 02:56 AM   #2
Location: Germany

Join Date: Oct 2016
Posts: 10

Hi! Is it really the exons only, that show reduced coverage and the rest of the genome shows 40x? Have you checked the mean of all exons or for one particular gene only? What kind of genome and data are you working with? In general I would say it's kind of normal to see differences in coverage over the genome, but I am not aware of a exon specific bias. However, if you look on a particular gene or even a gene-family, the coverage might be reduced because of homology regions and multimapped reads with low mapping quality that are filtered out. Maybe it is worth to have a look on the percentage of reads you are able to map against your reference. A high number of discarded sequences could be a hind of such an effect.
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