Figure 3.

Illustration of how a respective mapq threshold is chosen for each of our evaluated SSRs

The orange dot labeled ”mapq = 60″ shows the mapping error rate and fraction of reads mapped for HPC at mapq threshold 60. Anything below and to the right of this point is strictly better than HPC at mapq = 60, i.e. it has both a lower mapping error rate and higher fraction of reads mapped. If an evaluated SSR does not pass through this region, then it is discarded from further consideration. In the figure, the blue SSR does pass through this region, indicating that it is better than HPC at mapq = 60. We identify the leftmost point (marked as a blue dot) and use the mapq threshold at that point as the respective threshold.