Figure 3. The correlations between the aligners' assigned and actual mapping qualities.

Phred score scheme. (A) and (B) simulated datasets in 100 bp and 76 bp read lengths. (C) E. coli simulated dataset in which “MOSAIK” is MOSAIK's default mapping-quality network trained by human genome while “MOSAIK-retrained” is the retrained mapping-quality network by using E. coli simulation and E. coli genome. The detailed numbers of the Pearson's correlation coefficients are given in Table 3.