Summary of counterpart breakend calls. Breakends are called counterparts when they have a convergent (+, −) orientation and are close together on the genome. (A) (Left) Proportion of all breakends pairs in (+, −) orientation (y-axis) at varying distance thresholds D (x-axis), showing excess of convergent pairs at small distances. (Right) Proportion of breakend pairs with each of four possible orientations, at different distance thresholds D. The convergent (+, −) orientation is enriched at small distances (p <10−60 for D = 32bp, binomial test), suggesting that the breakend pairs are indeed counterparts, and unlikely to result from chance or frequent breakage at closely located sites. (B) A mild enrichment of divergent breakend pairs at intermediate distances (e.g. D = 2kb) suggests the occurrence of focal duplications resulting from copy-and-paste insertions at breakpoint junctions.