Evaluation criteria. An example showing how the different evaluation criteria work. In the upper part of the figure, the sequence in blue is the original genomic position where the simulated read was extracted from. After applying sequencing errors, the read does not exactly match to the original location (3 mismatches). In the lower part of the figure, three possible alignment locations for the read are shown with their mapping quality score (MQ). The naïve criterion would only consider the alignment (1) as the correct alignment. For Ruffalo et al.  criterion, if the used threshold is 30, then (1) is correctly mapped while (2) and (3) are incorrectly mapped-strict. On the other hand, if the threshold is 40, then (3) is considered as incorrectly mapped relaxed. Holtgrewe et al.  criterion in the oracle mode would detect (1) and (2) and consider them correctly mapped while (3) would be considered as incorrectly mapped.
Hatem et al. BMC Bioinformatics 2013 14:184 doi:10.1186/1471-2105-14-184