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) |