Inversion

A) Green and purple arrows show how reads derived from the variant genome are aligned to the reference genome. Red Stars indicate breakpoints in the variant genome and sites of split/hard-clipped reads in the reference genome alignment. Note that the paired reads spanning the breakpoints align to the same strand of the reference.

B) Characteristics of an inversion are indicated: (1) hard-clipped reads, and (2) paired reads mapping to same strand at the breakpoints.