Figure 2

Quality threshold estimation. EST assemblies were analyzed at different quality thresholds by removing those positions of the assemblies whose sum of qualities were below the threshold (see Methods). The average quality of the sequences in the remaining positions was plotted (y-axis) against the range of quality thresholds tested (x-axis). L – S. lycopersicum assemblies, LxH – assemblies including S. habrochaites and S. lycopersicum ESTs, LxP – assemblies including S. lycopersicum and S. pennellii ESTs. Maximum average sequence quality is achieved with thresholds of 40 for LxH and LxP and 50 for the L assemblies.