Although rates of CNV mutation have been well characterized at a small number of loci using experimental techniques, a reliable estimate of the genome-wide mutation rate has yet to be obtained. With a set of CNVs ascertained in a consistent manner we used the Watterson estimator of the population-scaled mutation rate, θW,to estimate the average per-generation rate of CNV formation, μ. The ascertainment-corrected number of segregating sites (>500 bp) leads to an estimate of μ = 3 × 10−2 mutations per haploid genome, per generation; however at the base-pair level, heterogeneity in this rate is expected to vary by several orders of magnitude among sites (Supplementary Methods). This estimate does not account for purifying selection, and so it probably represents a lowar bound on the true rate.
