Linkage Disequilibrium Calculator
Calculate linkage disequilibrium (D), D', and r² between two genetic loci.
Linkage Disequilibrium Calculation
Enter allele frequencies and haplotype frequency to calculate D, D', and r².
About Linkage Disequilibrium
Linkage disequilibrium (LD) is the non-random association of alleles at different loci in a given population. It is an important concept in population genetics and can provide insights into the evolutionary history of populations and the mapping of disease-causing genes.
LD Coefficient (D)
The LD coefficient (D) is calculated as the difference between the observed frequency of a haplotype and the expected frequency if the alleles were independently assorted:
D = pAB - (pA × pB)
Where pAB is the frequency of the AB haplotype, pA is the frequency of allele A, and pB is the frequency of allele B.
Normalized LD Coefficient (D')
D' (D prime) is the normalized linkage disequilibrium coefficient, providing a standardized measure that accounts for allele frequencies:
D' = D / Dmax
Where Dmax is the maximum possible value of D given the allele frequencies.
Correlation Coefficient (r²)
The correlation coefficient r² measures the proportion of variance at one locus that can be explained by variation at another locus:
r² = D² / (pA × (1 - pA) × pB × (1 - pB))