Detection of inversions of different sizes. (A) A summary of all inversion detection techniques presented in this paper and the conditions in which they are applicable. Small inversions will be evident as a sequence of SNPs or by a concentration of soft trimmed reads, while large inversions flanked by oversized IRs can be discovered by mate-pair WGS or by coverage trends. (B) Funnel detection in mate-pair data: gap size against genomic location plots centered on both ends of a mega-inversion. Mate-pair WGS with 2 kbp insert size reveals a funnel pattern in the boundaries of a suspected inverted segment. This funnel is not seen when using a 500 bp insert size. (C) PCR confirmation of the inversion. The wild-type (wt) and mutated strains were compared, using two sets of primers forward (F) and reverse (R), corresponding to both orientations. (D) Inversion detection by coverage trends. Coverage plots of the entire chromosome of the KLY mutant depict the average coverage of a genomic area against its location. Top: mapping to the reference genome reveals a 700 kbp disruption in the coverage trend caused by the mega-inversion. Bottom: mapping to a revised reference genome incorporating the mega-inversion negates the disruption. The origin of replication (ori) and replication terminus (ter) are indicated by arrows.