New quality scores for 454 reads. Old: quality scores from 454 software v.1.0.52. New: quality scores developed for this work. Data for panels A, B, and C come from 13 different runs on DNA from five different species. (A) Predicted vs. observed quality for old and new quality scores. New quality scores are much closer to the ideal, 1:1 line. (B) Proportion of bases greater than a given actual quality. The new quality scores accurately identify many more bases at quality ≥30 (63% vs. 23%). (C) Error prediction by error type. New quality scores accurately predict different types of errors: predicted vs. actual quality when errors are separated into overcalls, undercalls, and miscalls. (D) New quality scores are stable across machines. Predicted vs. actual quality for three runs of the same human BAC library on three different machines. (E) New quality scores are stable across genomes. Predicted vs. actual quality for five genomes varying in GC content and proportion of bases in homopolymers.
