Figure 1.

We plot the fraction of low quality reads in the 138 samples analyzed in our study. Across all samples the R2 reads harbor more low quality reads than the R1 reads. We plot two alternative definitions of ‘low quality’. Reads are called low quality if (A) the average Phred score is below 30, or (B) the average mismatch rate of the aligned bases is above 0.01. Both plots show that the R2 reads harbor more low quality reads and that the fraction of low quality reads is more variable across samples.