Fig. 3

Performance of McClintock 2 component methods in simulated yeast WGS data. Shown are the (A) recall and (B) precision across different fold-coverage for individual compnent methods to detect single synthetic insertions in an otherwise unmodified S. cerevisiae reference genome. Purple lines (Simulation 3) model the biologically realistic insertion preferences of yeast TEs, with synthetic Ty insertions created upstream of tRNA genes in regions that often have fragments of prior TE insertions in the reference genome. Orange lines (Simulation 4) model random insertions in non-repetitive regions, which allows insight into the effects of insertion within repetitive DNA and component’s performance for organisms without strong TE targeting preferences. Points indicate tested fold-coverage configurations, i.e, 3\(\times\), 6\(\times\), 12\(\times\), 25\(\times\), 50\(\times\) and 100\(\times\). Solid lines represent performance estimates for non-reference TE predictions made at the exact site of the synthetic insertion. Dashed lines represent performance estimates for non-reference TE predictions made within 100 bp surrounding the synthetic insertion site. The six original component methods in McClintock 1 are on the top row of each panel, and the six new methods in McClintock 2 are on the second row of each panel