The number of structural variants we observed declined rapidly with increasing variant length (Fig. 1d), with notable peaks corresponding to Alus and LINEs. The proportion of larger structural variants that was novel depended markedly on allele size, with variants 10 bp to 5 kb in size most likely to be novel (Fig. 1d). This is expected, as large (> 5 kb) deletions and duplications were previously discovered using array based approaches14, 20, whereas smaller structural variants (apart from polymorphic Alu insertions) had been less well ascertained prior to this study.
