For each variant, summary data for genotype quality, allele depth and population specific allele counts were calculated before removing all genotype data. This variant summary file was then functionally annotated using variant effect predictor (VEP) with the LOFTEE plugin. This data set can be accessed via the ExAC Browser (http://exac.broadinstitute.org) or downloaded from ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/ExAC.r0.3.sites.vep.vcf.gz. Full details regarding the annotation of the ExAC data set are described in the Supplementary Information Sections 1.9–1.10.
