The submitted SNP page contains the term “frequency of minor variant”. What does it mean?
The frequency of the minor variant is the minor allele frequencies for heterozygous and homozygous SNPs with reference to the frequency of all alleles at a particular SNP location. For example, suppose a SNP is genotyped on 50 individuals, with A/A=45 and G/G=5, the minor allele is therefore G with a frequency of 0.1. If the genotype count for the same 50 individuals was reported as A/A=43, A/G=4, and G/G=3, the minor allele would therefore be G, with a minor allele frequency still at 0.1.
