Coverage plot. Average read depth (times, in covered regions) is shown by columns and quantified on the left y-axis. Genome coverage (%) is shown by the black line and quantified on the right y-axis
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coverage-plot
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The last graph is Average alignments per read (Figure 5) and shows the average number of alignments for each read, with samples as columns. For single-end data, the expected average alignments per read is one, while for paired-end data, the expected average alignments per read is two.