than at homozygous sites. Again, performance of the approach with larger numbers of individuals improves because the mosaic fragments described by our model increase in length and, thus, become easier to find. This is also reflected in the accuracy of estimated haplotypes, which—when compared with simulated haplotypes—have ~1 switch per 50 kb when 100 individuals are examined, but ~1 switch per 500 kb when 400 individuals are examined. We expect that combining shotgun re-sequencing of whole genomes with imputation-based approaches such as ours will allow economical association studies that evaluate SNP variation in large numbers of individuals even more exhaustively than is currently possible. Furthermore, we expect that whatever the characteristics of the re-sequencing technology used, it will be possible to improve the quality of estimated genotypes and haplotypes at each site by combining information across individuals, rather than simply increasing the depth at which each individual is sequenced.
