We additionally specifically assessed the complexity of the 29,954 deletions with resolved breakpoints and found that 6% (1,822) intersected another deletion with distinct breakpoints. A larger fraction (16% or 4,813 of assembled deletion sites) showed the presence of additional inserted sequence at deletion breakpoints. We grouped 1,651 deletions with mean size of 3.1 kbp and at least 10 bp of additional DNA sequence between the original SV site boundaries into five broad classes (Fig. 3b, Supplementary Table 12). The most common class (n = 501, 30.3%), termed ‘Ins with Dup and Del’, comprised deletions exhibiting a recognizable duplicated sequence interval within the respective inserted sequence. Notably, in many cases (n = 191) the inserted sequences comprised two or more apparent sequence duplications at the deletion boundaries (a class denoted ‘Ins with MultiDup and Del’). Additional classes commonly observed include Inv and Del (inversion with adjacent deletion; n = 9) and ‘MultiDel’—a class where two or more adjacent deletions are separated by at least one sequence ‘spacer’ of up to ∼204 bp in length (n = 370). However, not all complex
