引用自NCBI的概念（https://www.ncbi.nlm.nih.gov/projects/SNP/docs/rs_attributes.html#gmaf）
Global minor allele frequency (MAF): dbSNP is reporting the minor allele frequency for each rs included in a default global population. Since this is being provided to distinguish common polymorphism from rare variants, the MAF is actually the second most frequent allele value. In other words, if there are 3 alleles, with frequencies of 0.50, 0.49, and 0.01, the MAF will be reported as 0.49. The current default global population is 1000Genome phase 3 genotype data from 2500 worldwide individuals, released in the May 2013 dataset.
For example, refSNP page for rs222 reports: "MAF/MinorAlleleCount:G=0.249/542". This means that for rs222, minor allele is 'G' and has a frequency of 24.9% in the 1000Genome phase 1 population and that 'G' is observed 542 times in the sample population of 1088 people (or 2176 chromosomes).
首先需要了解一下 allele frequency（等位基因頻率）的概念。用一個例子說明：假設在100個人里面，某條染色體上某個位點有一個SNP，這個SNP位點有三個allele： A, C, G。 通過全基因組測序的方法我們發現這100個人里面這個位點的鹼基A出現100次，C出現80次，G出現20次（人是二倍體，因此這個SNP位點有200個）。所以我們可以計算這三個allele的頻率: A = 100/200, C = 80/200, G = 20/200. 那么根據定義，出現第二多的就是minor allele frequency。 也就是allele C，MAF為0.4。