Next, to better understand what parts of the genome were undercovered, we generated GC-bias plots (Figure 2), showing relative coverage at each GC level (and for context, the fraction of the genome at each level). These plots provide fine detail but also mirror the preceding conclusions, exhibiting the same hierarchy at GC extremes. For example, Ion Torrent coverage dropped severely below 10% and above 75% GC. On the other hand, all three technologies provided nearly even coverage of the moderate-GC range (30 to 70%) in E. coli. At the lowest GC, even Pacific Biosciences showed approximately two-fold coverage reduction, perhaps attributable to dissociation of fragment ends in adapter ligation, a phenomenon that could apply to all three technologies.
