To estimate the effectiveness of common variant discovery in the pooled sequencing analysis, we determined the number of known HapMaP SNPs with a frequency >0.10, and >0.20 that were detected by pooled genomic sequencing in our sample. At these thresholds, we detected respectively 85% and 87% of known CEU HapMaP SNPs. These data suggest that the efficiency of mutation discovery was good for alleles with MAF >0.10. Moreover, as discussed above, given the coverage we already had for the novel SNPs we detected, it is unlikely that detection of additional SNPs would have provided much additional genetic information with respect to common alleles.
