FIG 3 .
Deep sequence coverage of HSV-1 variants from each strain group. Preprocessed sequence reads were aligned to the new draft genomes to assess the coverage depth of each assembly. Coverage depth is plotted on a log10 scale (y axis) across the length of the HSV-1 genome (x axis). Major regions of the HSV-1 genome are diagrammed below the x axis, including the long and short internal repeats (IRL and IRS). Genomes and coverage are shown in a trimmed format (12), where the terminal copies of IRL and IRS are not included. Coverage tracks are overlaid for (A) HSV-1 KOS variants, (B) HSV-1 F variants, and (C) HSV-1 H166 and H166Syncytial. The total number of sequence reads obtained was different for each HSV-1 strain, which affects overall coverage depth (Table 3). However, peaks and valleys of coverage depth fall in similar locations on the HSV-1 genome, with the internal repeats (IRL and IRS) showing the most variability in coverage.