Peak FDR versus level of duplicate reads in six H3K27me3 ChIP-Seq libraries. Peaks were ranked based on –log10 (FDR) in descending order and split into 10 groups (x-axis) of equal size. The y-axis represents the level of duplicate reads. The horizontal dashed lines indicate the level of duplication from non-peak regions, as defined in Figure 3. The two biological replicates are indicated by r1 and r2, respectively.