科普笔记16 minor allele frequency 次等位基因频率

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（等位基因频率）的概念。用一个例子说明：假设在100个人里面，某条染色体上某个位点有一个SNP，这个SNP位点有三个allele： A, C, G。 通过全基因组测序的方法我们发现这100个人里面这个位点的碱基A出现100次，C出现80次，G出现20次（人是二倍体，因此这个SNP位点有200个）。所以我们可以计算这三个allele的频率: A = 100/200, C =  80/200, G = 20/200.  那么根据定义，出现第二多的就是minor allele frequency。 也就是allele C，MAF为0.4。