Table 2.

Minor allele load procedures

Procedure	Analytic description
All SNPs	All minor alleles counted
MAF ≥ 0.05	Only alleles with MAF ≥ 0.05 counted (T)
MAF < 0.05	Only alleles with MAF < 0.05 counted (T)
MAF < 0.01	Only alleles with MAF < 0.01 counted (T)
Inverse weighting	Exponentially increasing weight to rarer alleles (W)
Variable threshold	Empirically defined MAF level used as threshold. Significance drawn through permutation analysis (T)
Nonsynonymous/synonymous	Nonsynonymous and synonymous SNPs examined separately (F)
Functional weighting	SNPs weighted by degree of amino acid change derived from BLOSUM (WF)

T, threshold procedure; W, weighting procedure; F, function-based procedure.