The majority of variants in the data set are rare: ∼64 million autosomal variants have a frequency <0.5%, ∼12 million have a frequency between 0.5% and 5%, and only ∼8 million have a frequency >5% (Extended Data Fig. 3a). Nevertheless, the majority of variants observed in a single genome are common: just 40,000 to 200,000 of the variants in a typical genome (1–4%) have a frequency <0.5% (Fig. 1c and Extended Data Fig. 3b). As such, we estimate that improved rare variant discovery by deep sequencing our entire sample would at least double the total number of variants in our sample but increase the number of variants in a typical genome by only ∼20,000 to 60,000.
