To further explore inversion sequence complexity, we performed a battery of targeted analyses, leveraging PacBio resequencing of fosmids (targeting 34 loci), sequencing by Oxford Nanopore Minion (60 loci) and PacBio (206 loci) of long-range PCR amplicons, and data for 13 loci from another sample (CHM1) sequenced by high-coverage PacBio WGS14. Altogether we verified and further characterized 229 inversion sites, 208 using long-read data and 21 by PCR (Supplementary Table 15), increasing the number of known validated inversions21 by >2.5-fold. Remarkably, only 20% of all sequenced inversions characterized in this manner were ‘simple’ (termed ‘Simple Inv’), exhibiting two breakpoints (Fig. 3e), including a 2 kbp inversion on chromosome 4 intersecting a regulatory exon of the Ras homologue family member RHOH (Fig. 3d, right panel). The majority of inversions (54%) corresponded to inverted duplications (‘Inverted Dup’; Fig. 3d, middle right panel). In nearly all cases, these involved duplicated stretches <1 kbp inserted within 5 kbp of the alternate copy, suggesting a common mechanism of SV formation (Extended Data Fig. 10). The remaining inversions comprised ‘Inv and Del’ events (14%), ‘MultiDel’ events exhibiting
