Fig. 5.

Recalibration of base quality scores using monomorphic sites improves performance. (A) Reported base quality scores do not match empirical scores calculated from real data using monomorphic sites. (B) The EM algorithm was run with and without base quality score recalibration on simulated pooled 100-bp paired-end sequence data from 162 haplotypes at 200× coverage in a 200 kb region (100 replicates each). Sequence errors in the simulated data were introduced with probabilities given by the empirical error rates.