Supplementary Figure 2: CCS read accuracy and coverage uniformity.

(a) Distribution of accuracy predicted by the CCS algorithm for reads with fewer than 3 passes and at least 3 passes, which we consider a minimum pass count for CCS. Approximately half of reads have 3 or more passes; among those nearly all achieve Q20 predicted accuracy. (b) Distributions of HG002 concordance, measured against the GIAB benchmark, at levels of predicted read accuracy (R² of median = 0.9980). Orange lines are medians; boxes extend from lower to upper quartiles; whiskers extend 1.5 interquartile distances; n=1,000 reads at each predicted accuracy. (c) Distribution of difference between concordance and predicted read accuracy shows that the prediction is well-calibrated to the empirical concordance. (d) Distribution of coverage in 500 bp windows at non-gap positions in GRCh37. (e) Coverage distributions at levels of [GC] content, measured in 500 bp windows. Orange lines are medians; boxes extend from lower to upper quartiles; whiskers extend 1.5 interquartile distances; n per distribution is listed above the plot.