Table 1 shows the numbers of SNPs attempted and converted to QC+ SNPs in each analysis panel (Supplementary Table 5 shows a breakdown by each major submission). Haplotypes and missing data were estimated for each analysis panel separately using both trio information and statistical methods based on the coalescent model (see Methods). To enable cross-population comparisons, a consensus data set was created consisting of 3,107,620 SNPs that were QC+ in all analysis panels and polymorphic in at least one analysis panel. The equivalent figure from Phase I was 931,340 SNPs. Unless stated otherwise, all analyses have been carried out on the consensus data set. An additional set of haplotypes was created for those SNPs in the consensus where a putative ancestral state could be assigned by comparison of the human alleles to the orthologous position in the chimpanzee and rhesus macaque genomes.
