Figure 1 |

Mapping reads to a reference genome accounting for uniqueness. In step 1, each read is aligned against the reference genome. In the second step, the quality of each read is weighted according to the uniqueness of the hit. A read giving rise to two hits S₁ and S₂ in the reference genome will be weighted proportionally with the relative alignment scores; if scores are identical, the mapping of S₁ and S₂ will be applied a weight of w=0.5 (see equation below). Step 3 maps the weighted qualities back to the reference genome so that each genomic position contains an array of weighted qualities. Once all reads are mapped, in step 4 only the maximum weighted quality value is kept and, step 5, the maximum weighted quality scores are color coded to reveal regions of low uniqueness.