As expected, the vast majority of sites variant in any given individual were already present in dbSNP; the proportion newly discovered differed substantially among populations, variant types and allele frequencies (Fig. 1). Novel SNPs had a strong tendency to be found only in one analysis panel (Fig. 1a). For SNPs also present in dbSNP version 129 (the last release prior to 1000 Genomes Project data), only 25% were specific to a single low coverage analysis panel and 56% were found in all panels. On the other hand, 84% of newly discovered SNPs were specific to a single analysis panel whereas only 4% were found in all analysis panels. In the exon project, where increased depth of coverage and sample size resulted in a higher fraction of low frequency variants among discovered sites, 96% of novel variants were restricted to samples from a single analysis panel. In contrast, many novel SVs were identified in all analysis panels, reflecting the lower degree of previous characterisation (Supplementary Figure 4).
