The MARKER map displays various measure of linkage disequilibrium for a pair of biallelic loci. (In future versions we will include multiallelic loci.) Here we show how we calculated the different metrics. Please let us know if you spot any errors, or if you have another metric that you'd like us to include.
In these help pages:
- A and a denote the alleles at the first locus (where A is major)
- B and b denote the alleles at the second locus (where B is major)
- thus fAb is the frequency of the haplotype carrying the major allele for the first locus and the minor allele for the second locus.
Sometimes we used a different convention when programming so you may come across data labelled like this:
f
11 = f
AB = frequency of haplotype of major alleles
f
12 = f
Ab = frequency of haplotype of major and minor alleles
f
21 = f
aB = frequency of haplotype of minor and major alleles
f
22 = f
ab = frequency of haplotype of minor alleles
References
