the 10-20x used in previous applications of these technologies to whole genome resequencing. To accurately call polymorphisms in each genome, the Project will then use imputation based techniques to combine information across individuals who share a particular haplotype stretch. Using simulations, we have predicted that when 400 diploid individuals are sequenced at only 2x depth (1x per haploid genome) and the data is analyzed using approaches that combine data across individuals sharing similar haplotype stretches, polymorphic sites with a frequency of >2% can be genotyped with >99.5% accuracy (Li and Abecasis; unpublished data). Note that the same 2x average depth would not be useful for genotype calling when examining a single individual – since, by chance, ~50% of alleles would not be sampled. For another example of how genotype imputation can be combined with sequence data, see (72).
