Figure 2.

Increase of R2 low quality reads as a function of the content of long fragments. In (A) we plot for individual samples the difference in low quality read content among the R2 and the R1 reads versus the content of long fragments. The plot shows that the more long fragments a samples has the more prevalent are low quality reads among the R2 reads. In (B) we directly compare the fraction of low quality reads in R2 and R1 and color-code the content long fragments. Low quality reads are defined as reads having a mismatch rate above 0.01 in the bases after alignment. The plotted samples have been generated using various protocols on various sequencers in various labs. The dashed lines connect three samples each that have been processed identically except with an increasing targeted fragment length.