6.3 years ago by
Loci are selected for a genotype assay such as a SNP chip because they are expected not to be uniform in the population. Most chips distinguish between two genotypes at a given locus; those are the two alleles. We can estimate the frequency of these alleles in the total population from their frequency in a sample population, such as the HapMap samples. One of these alleles will appear less frequently than the other; that is the minor allele. Typically GWAS are designed to exclude SNPs with a MAF < 5%, as it requires very strong statistical power to make meaningful statements about very rare alleles.
To a first approximation, you've correctly interpreted the result of a MAF of zero. In truth since we're just estimating the MAF, there may well be people who do not have the major allele.