allele frequency and achieve more than 90% accuracy. Although SNPs with low minor allele frequencies (MAF<5%) are referred to as uncommon SNPs, they represent more than 30% of SNPs in the HapMap Phase II CEU population, and this proportion is even higher in African populations[2]. This problem assessing imputation accuracy in lower frequency SNPs means that a large part of the genome will not be adequately interrogated using imputation.
