Fig. 1

The dependence of coverage on GC content. The coverage across regions of the genome with differing GC content compared using two different sequencing technologies; the Ion PGM and the Illumina MiSeq. The dashed blue line represents the cutoff used when calling variants. Any position which had a coverage <10 was marked as missing. The dashed red line shows at which GC% the median coverage across the window falls below the cutoff