So far, WGAS have been limited to SNPs with minor allele frequencies (MAF) greater than about 5%. Rare variants, being mostly neutral or nearly neutral, will often be founders and so relatively population specific. They are distinguished from clearly deleterious mutations by having frequencies that lie somewhere between ∼0.1%, the upper limit for deleterious mutations, and ∼1%, the lower limit of polymorphic variation. These frequency boundaries are, however, not absolutely defined, so there is likely to be some overlap at the margins between low-frequency common variants and high-frequency rare variants.
