Figure 3

Relationship between pooled allele frequency estimates and allele frequencies determined by individual genotyping. The frequency estimates from pooled genotyping, $\widehat{p}$, are linearly related to allele frequencies, p, determined by individual genotyping. (A) Across all SNPs that were individually genotyped, variation in slope and intercept partially obscures the strength of this relationship. Here, we show $\widehat{p}$ plotted against p averaged over the four high-density lipoprotein pools for 284 SNPs. (B) For each SNP, we have independent measurements of p and $\widehat{p}$ in four pools. We show representative data for four SNPs having (due to sampling variation or association) relatively large separation between the four values of p.