What does a LOD score measure?

A LOD score is the base-10 logarithm of the odds comparing a linkage model at a chosen theta with no linkage at theta = 0.5.

How is the estimated recombination fraction calculated?

The maximum-likelihood estimate is theta-hat = r/N, where r is the recombinant count and N is the total of recombinant and non-recombinant meioses.

What does a LOD score of 3 or higher mean?

A LOD score of at least 3 is classic evidence supporting linkage, corresponding to odds of at least 1000:1.

What does a LOD score of -2 or lower mean?

A LOD score of -2 or lower is classic evidence against linkage at the evaluated theta.

Is this calculator intended for clinical diagnosis?

No. The calculator is provided for educational use only and does not replace professional genetic analysis.

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LOD Score Calculator (linkage analysis)

Two-point linkage LOD scores from recombinant/non-recombinant meioses: θ̂ = r/N, Zmax, LOD at fixed θ, LOD curve table, Morton thresholds (Z≥3 linkage, Z≤−2 excluded). Derived from Morton 1955, Ott 1999, Griffiths, StatPearls. Educational use only.

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Significant linkage: 2 recombinants in 20 meioses (Zmax = 3.20)

A phase-known linkage sample with 2 recombinant and 18 non-recombinant meioses. The MLE recombination fraction is θ̂ = 2/20 = 0.10, and the maximum LOD is Zmax = log10[0.1²×0.9¹⁸ / 0.5²⁰] = 3.197. Since Zmax ≥ 3, this is significant evidence for linkage (odds ≥ 1000:1) at roughly 10 cM.

{"result":"LOD analysis: 2/20 recombinants, θ̂=0.1, Zmax=3.197 → significant evidence FOR linkage.","metadata":{"input":{"recombinantCount":2,"nonRecombinantCount":18},"result":{"mleTheta":0.1,"maxLod":3.197,"conclusion":"significant evidence for linkage"}}}

Linkage excluded: 10 recombinants in 20 meioses (LOD = −4.44 at θ = 0.1)

An unlinked marker gives 10 recombinant and 10 non-recombinant meioses (r/N = 0.5, the free-recombination expectation). Evaluating at θ = 0.1: LOD = log10[0.1¹⁰×0.9¹⁰ / 0.5²⁰] = −4.437. Since the LOD ≤ −2 at this θ, linkage at 10 cM is excluded; at θ̂ = 0.5 the LOD is 0, consistent with no linkage.

{"result":"LOD analysis: 10/20 recombinants, LOD(0.1)=−4.437 → significant evidence AGAINST linkage at θ=0.1.","metadata":{"input":{"recombinantCount":10,"nonRecombinantCount":10,"theta":0.1},"result":{"lod":-4.437,"conclusion":"significant evidence against linkage"}}}

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Theta ModeselectRequiredReport the maximum LOD at θ̂ = r/N, or evaluate the LOD at a fixed θ.Recombinant countnumberRequiredNumber of recombinant meioses observed (r).Non-recombinant countnumberRequiredNumber of non-recombinant meioses observed.Recombination fraction θnumberRequiredRecombination fraction at which to evaluate the LOD in fixed-θ mode (0 < θ < 0.5).Decimal PlacesnumberOptional

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LOD Score Calculator (linkage analysis)

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1. Significant linkage from 2 recombinant meioses

2. Evaluate linkage at a fixed theta

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