Use LD Coefficient D when you need to compute linkage disequilibrium coefficient D = f(AB) - p(A) * p(B); the signed result may be negative. Enter Haplotype AB frequency, Allele A frequency, and Allele B frequency using the definitions and units below so the result can be reproduced.

Haplotype AB frequency

A finite measured or assumed value from 0 through 1.

Allele A frequency

A finite measured or assumed value from 0 through 1.

Allele B frequency

A finite measured or assumed value from 0 through 1.

The published tool contract uses this rule: Compute linkage disequilibrium coefficient D = f(AB) - p(A) * p(B); the signed result may be negative.^[1]

LD coefficient D

The calculated ld coefficient d.

The calculation does not propagate measurement uncertainty, sampling error, or biological and chemical variability. Haplotype AB frequency must remain between 0 and 1; Allele A frequency must remain between 0 and 1.

Retain the original Haplotype AB frequency, Allele A frequency, and Allele B frequency values and their units alongside the result. LD R-Squared is useful when you instead need to compute squared linkage disequilibrium r2 = D^2 / (p(A) * (1 - p(A)) * p(B) * (1 - p(B))). Inbreeding Coefficient provides another view by helping you compute the inbreeding coefficient f = (he - ho) / he, which may be negative when heterozygote excess occurs.

• LD R-Squared

  Compute squared linkage disequilibrium r2 = D^2 / (p(A) * (1 - p(A)) * p(B) * (1 - p(B))).

• Inbreeding Coefficient

  Compute the inbreeding coefficient f = (he - ho) / he, which may be negative when heterozygote excess occurs.

• Coancestry Coefficient

  Compute the coancestry or kinship phi of two individuals as half of their additive relationship coefficient.