Figure 1.
An example of an incorrect long read alignment to the reference genome and its correction. If a donor genome (above) contains two copies of CYP2D6 pharmacogene, any long read (gray rectangle) that spans both copies will get aligned to the reference genome (below) that contains only a single CYP2D6 copy. However, this read will get its second half (containing CYP2D6 sequence) incorrectly aligned to the CYP2D7 pseudogene owing to the high sequence similarity between these genes. The final result is the overabundance of coverage in the pseudogene region compared with the CYP2D6 region (an Integrative Genomics Viewer [IGV; Robinson et al. 2011] coverage plot is shown above the reference genome).
