As expected, nearly all of the high frequency SNPs discovered here were already present in dbSNP; this was particularly true in coding regions (Fig. 1c). The public databases were much less complete for SNPs at low frequencies, for short indels and for structural variants (Fig. 1d). For example, in contrast to coding SNPs (91% of common coding SNPs described here were already present in dbSNP), approximately 50% of common short indels observed in this project were novel. These results are expected given the sample sizes used in the sequencing efforts that discovered most of the SNPs previously in dbSNP, and the more limited, and lower resolution, efforts to characterize indels and larger structural variation across the genome.
