Figure 5

Average base quality scores. A. The estimated quality values produced by the GS Junior were compared to the empirical quality values calculated by error frequencies. The thin red line marks the ideal line if the system would estimate all values correctly. B. Development of base quality scores (averaged per position) over the reads’ lengths (and run progress). Comparison of six runs (thin red lines) and their average (bold dark red line). The quality drop at the first 20 bases is no application specific phenomenon but explained by the mathematical calculation of the quality scores and their dependence on previous flows and bases.