The tendency for deleterious functional variants to have lower allele frequencies has consequences for the discovery and analysis of this type of variation. In the deeply sequenced CEU trio father, who was not included in the low coverage project, 97.8% of all single base variants had been found in the low coverage project, but only 95% of nonsynonymous, 88% of stop inducing and 85% of HGMD-DM variants. The missed variants correspond to 389 nonsynonymous, 11 stop inducing and 13 HGMD-DM variants. As sample size increases, the number of novel variants per sequenced individual will decrease, but only slowly. Analyses based on the exon project data (Fig. 3) showed that on average 99% of the synonymous variants in an individual would be found in 100 deeply sequenced samples, whereas 250 samples would be required to find 99% of nonsynonymous variants and 320 samples would still find only 97.4% of the LOF variants present in an individual. Using detection power data from Fig. 2a, we estimated that 250 samples sequenced at low coverage would be needed to find 99% of the synonymous variants in an individual, and with 320 sequenced samples 98.5% of nonsynonymous and 96.3% of LOF variants would be found.
