Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability

[...]Watson et al. bring up mappability of reads as a confounding factor while failing to mention that the original paper [1] considered and--using bisulfite sequencing data from embryonic stem cell H1 as a control--ruled out ascertainment biases due to read mappability: "We next examined the difference in methylation levels between sperm and H1. [...]Watson et al. argue that the higher mode with zero scores for the Methylation Index (MI = 0) is likely an artifact due to small SNP and CpG counts.