Fig. 6

SVs identified by OMSV from C666-1. a Overlap between the large (>2 kbp) indels identified by OMSV and the two short-read-based callers, Manta and Pindel. In the common regions, the number of a certain color indicates the number of SVs called by the respective method that overlap SVs called by the other method(s). b–d Polymerase chain reaction results for selected homozygous insertions (b), heterozygous insertions (c), and complex SVs (d). For the heterozygous insertions, I _e2 was tested separately from the other six cases due to the large expected product size of its insertion allele. For the inversion case C ₃, p1 and p2 correspond to the two primer pairs. e Alignment of sequencing reads to the inferred C666-1 sequences of SV I _o2 and SV I _o3. The L and R boxes mark the primer locations. Definitions of o ₁, o2′, b1′, b2′, g1′ and g2′ are given in Additional file 1: Figure S9. Sequencing read alignments are visualized by IGV [49]. SV, structural variation