Duplication

A) Green 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 tandem duplication breakpoint align in an inverted orientation.

B) Characteristics of a tandem duplication are indicated: (1) increased read depth proportional to copy number, (2) hard-clipped reads, and (3) inverted read pair orientation spanning breakpoints.