Linkage Disequilibrium Calculator

Linkage disequilibrium (LD) measures how often two genetic variants appear together on the same chromosome more (or less) than chance would predict — a key concept in population genetics and genome-wide association studies. Enter the frequency of Allele A, frequency of Allele B, and the observed AB haplotype frequency into the Linkage Disequilibrium Calculator to get the LD Coefficient (D). Secondary outputs include the normalized D' (D Prime), correlation coefficient (r²), and the expected AB haplotype frequency under random association.

Enter the frequency of allele A in the population (0-1)

Enter the frequency of allele B in the population (0-1)

Enter the observed frequency of AB haplotype (0-1)

Results

LD Coefficient (D)

--

Normalized D' (D Prime)

--

Correlation Coefficient (r²)

--

Expected pAB Frequency

--

More Biology Tools

Frequently Asked Questions

What is linkage disequilibrium (LD)?

Linkage disequilibrium is the non-random association of alleles at different loci in a population. When alleles at two loci appear together more or less frequently than expected by chance, they are said to be in linkage disequilibrium.

How is the LD coefficient (D) calculated?

The LD coefficient D is calculated as D = pAB - (pA × pB), where pAB is the observed frequency of the AB haplotype, pA is the frequency of allele A, and pB is the frequency of allele B. It measures the difference between observed and expected haplotype frequencies.

What does D' (D prime) represent?

D' is the normalized LD coefficient that ranges from 0 to 1, making it easier to compare LD across different allele frequency combinations. D' = 1 indicates complete linkage disequilibrium, while D' = 0 indicates linkage equilibrium.

What is r² and why is it important?

r² is the correlation coefficient between alleles at two loci, ranging from 0 to 1. It measures how well one locus can predict another and is particularly important in genetic association studies for determining how well a marker SNP represents variation at nearby loci.

What causes linkage disequilibrium in populations?

LD can be caused by several factors including physical proximity of loci on chromosomes, population bottlenecks, population structure, natural selection, and recent mutations. The closer two loci are physically, the more likely they are to be in LD.

How do I interpret negative D values?

Negative D values indicate that the AB haplotype occurs less frequently than expected by chance, meaning there is negative association between alleles A and B. This suggests that these alleles tend to avoid being inherited together.

What is the difference between D and r²?

D measures the absolute deviation from independence, while r² measures the proportion of variance in one locus explained by another. r² is more commonly used in association studies because it directly relates to statistical power for detecting associations.

Can linkage disequilibrium exist between unlinked genes?

Yes, LD can exist between genes on different chromosomes due to population structure, admixture, or selection. However, recombination will eventually break down LD between unlinked loci over many generations.