We used data from the HapMap project Phase II to estimate coverage. Single marker coverage was defined to be the proportion of all variation (with minor allele frequency greater than 5%) in r 2 with a SNP on the genotyping chip above 0.8. Using this definition we achieved very similar estimates to previous studies which used the whole genome (we use twenty two representative megabases). Multi-marker coverage was calculated by an aggressive search of all 2-SNP and 3 SNP haplotypes within 250kb of the SNP being tagged [6]. The SNP was tagged if any of these multi-marker tags had r2 above 0.8, the rule defining the haplotype was also stored and added to the list of multi-marker tests.
