Quality threshold vs. number of mismatches. Mapping 1 million reads of length 125 extracted using wgsim from the Human genome while allowing up to 7 mismatches and a quality threshold of 140. The error is 0.6% for SOAP2 and MAQ and 0.45% for GSNAP.
Hatem et al. BMC Bioinformatics 2013 14:184 doi:10.1186/1471-2105-14-184