Translocation

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 map to different molecules when aligned to the reference genome.

B) Characteristics of a translocation are indicated: (1) hard-clipped reads, and (2) mates mapping to a different molecule. The two windows shown are located on different chromosomes.