Genome-wide, 469,557 SNPs (93.8%) passed our quality control filters (described in Methods) giving an average call rate of 99.63%. Of those, 392,575 have study-wide MAFs > 1% (45,106 have MAFs < 0.1%; see also Supplementary Figs 1 and 2). Initial analyses of the polymorphic SNPs suggest that patterns of linkage disequilibrium in our samples are very similar to those in HapMap (Supplementary Fig. 3). Therefore, we expect genome coverage with the Affymetrix 500K set in this study to be similar to that estimated for the HapMap CEU panel2.
