A tandem duplication identified in a var gene region of the AT-rich Plasmodium falciparum. Coverage is shown for two samples of P. falciparum—a genetically modified line (C5), which was derived from the parental laboratory strain (3D7). The AT-rich genome shows high coverage in genes, which drops to very low levels in the AT-rich nonexonic regions. A change in copy number is apparent in the C5 coverage. GRIDSS detected the underlying tandem duplication in the C5 vaccine candidate (indicated). The supporting discordant read pair (DP) evidence is shown for both strains. Weak evidence (one read pair) for this rearrangement was also detected in the parental population, indicating that the SV was subclonal in this population. This evidence contributed to the positional de Bruijn graph assembly.
