Figure 3.

Comparison of sequencing depth and variation in mutually targeted regions. A: Normalized coverage was calculated (reads per million sequenced reads) (y axis) for each mutually targeted base and plotted average (blue) and SD (red) versus genomic positions (x axis). Read count was obtained from Sequence Alignment/MAP (SAMtools) mpileup files. B: Plot of percentage of mutually targeted bases that were covered at average minimum normalized coverages (solid lines). An ideal curve is included for each technology (dotted lines), where the average normalized sequencing is uniformly distributed for each technology. Different technologies have different average normalized coverages, so ideal curves will be different between technologies. Solid lines should be compared to dotted lines for the respective technology. C: Average normalized coverage is plotted against the percent GC content in 100-bp windows. Darker colors indicate higher density of points, whereas lighter colors indicate lower density of points.