Fig. 2.

Samplot images of duplication, inversion, and translocation variants. a A duplication variant plotted by Samplot with Illumina short-read sequencing evidence. Reads plotted in red have large insert sizes and inverted pair order (reverse strand followed by forward strand instead of forward followed by reverse), indicating potential support for a duplication. b An inversion variant, with Illumina sequencing evidence. Reads plotted in blue have large insert sizes and same-direction pair alignments (both reads on forward strand, or both on reverse strand). c A translocation variant, with Illumina sequencing. Discordant pairs align to each breakpoint. The blue color of the reads and extremely large insert sizes of these grouped discordant pairs indicate a large inverted translocation