Fig. 8

Simulation of mapping with mismatches. a In this simulation, three 56-bp artificial gene sequences were created. Two sequences (blue) were identical except at two nucleotide positions (marked as X, position not in scale). From each artificial gene, 1000 full-length reads were generated with base substitution errors. The reads were mapped back to the reference, and only uniquely mapped reads were accepted. b Four different error rates used for the simulation and the resulting mapping percentage, either when only perfect match is allowed (brown) or when up to two mismatches are allowed (green). c The fractions of uniquely mapped reads in the three genes illustrated in (a). The grey scale indicates one of the three genes. The column labels A-D indicate independent simulations with the error rates indicated in (b). ‘Perfect match’ allowed only perfect matching alignment. ‘2 mismatches, all’ accepts all alignments up to 2 mismatches. ‘2 mismatches, best’ accepts all the alignments with the minimum number of mismatches for each read