What LOD score indicates linkage?

A LOD score of 3 or higher is commonly treated as strong evidence for linkage.

What does a negative LOD score mean?

It means the data are more likely under no linkage than under the selected linkage model.

What is θ in linkage analysis?

Theta is the recombination fraction between two loci. It ranges from 0 to 0.5.

Can I use this for a full pedigree study?

Use this calculator for simple learning examples. Full pedigree analysis should use dedicated genetic linkage software.

LOD Score Calculator

Estimate the logarithm of odds for genetic linkage at a selected recombination fraction and compare the result with common LOD interpretation thresholds.

Non-recombinant observations

Recombinant observations

Recombination fraction θ

0-0.5

LOD Score Formula

LOD(θ) = log10(L(linkage at θ) / L(no linkage))

A LOD score compares the likelihood of observing the data if two loci are linked at recombination fraction θ with the likelihood if they are unlinked. This simplified calculator uses counts of non-recombinant and recombinant observations.

Symbol	Variable	Description
θ	Recombination fraction	Probability of recombination between two loci; values near 0 indicate tight linkage and 0.5 indicates no linkage.
LOD	Logarithm of odds	Base-10 log of the linkage likelihood ratio.
10^LOD	Odds ratio	How many times more likely the linkage model is than no linkage under the selected θ.

How to Use the LOD Score Calculator

1
Enter observations
Enter non-recombinant and recombinant observations from your linkage dataset.
2
Choose θ
Use a recombination fraction between 0 and 0.5. Lower θ values represent tighter linkage.
3
Compare thresholds
Review the LOD score, odds ratio, and interpretation against the common +3 and -2 thresholds.

What a LOD Score Means

A positive LOD score favors linkage at the selected recombination fraction. A negative LOD score favors no linkage. The scale is logarithmic, so a LOD score of 3 corresponds to odds of about 1000:1 in favor of linkage.

Why Theta Matters

The same dataset can produce different LOD scores at different θ values. In real linkage mapping, analysts often calculate LOD across a range of θ values and report the maximum LOD score and its corresponding recombination fraction.

Use This as a Teaching Calculator

This LOD score calculator is intended for learning and quick checks. Full pedigree linkage analysis can require penetrance models, marker phase, sex-specific recombination, and specialized software.

LOD Score FAQ

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