Fig. 4

Concordance of IL methods compared against total IL callset and PB callset using orthogonal technologies. Results by algorithm shown for a the deletion concordance for individual methods, b the union of all pairs of methods, and c the requirement that more than one caller agree on any call. Individual callers are shown as red points for comparison. Pairs and triples of combinations are in black points. The solid and dashed lines represent the 5% and 10% non-concordance rates (NCR), respectively. The top five combinations of methods in each plot below the 10% NCR, along with the individual plots, are labeled. d Overlap of IL-SV discovery algorithms, with total number of SVs found by each combination of IL algorithms (gray) and those that overlapped with the PB-SV calls (blue) in the YRI child NA19240. e PCA of the genotypes of concordant calls of each method: PC 1 versus 2 (left), PC 2 versus 3 (right). VH VariationHunter