LOD Score Calculator (linkage analysis)

LOD Score Calculator (linkage analysis) | Online Free Tool | Elysia Tools

Tool usage guide

Learn when to use this tool, what it supports, and how real users apply it.

Key facts

Category: Education
Input types: select, number
Output type: json
Sample coverage: 4
API ready: Yes

Overview

The LOD Score Calculator performs educational two-point linkage analysis from recombinant and non-recombinant meioses. It estimates the recombination fraction, calculates the maximum LOD or LOD at a fixed theta, and interprets results using classic linkage thresholds.

When to use

Estimate the recombination fraction and maximum LOD from observed recombinant and non-recombinant meioses.
Evaluate evidence for or against linkage at a specific recombination fraction theta.
Use classic LOD thresholds to support, exclude, or assess uncertainty about two-point genetic linkage.

How it works

1Choose Maximum LOD to estimate theta as the recombinant count divided by the total meioses, or choose fixed-theta mode.
2Enter the recombinant count and non-recombinant count from the linkage sample.
3In fixed-theta mode, enter a theta value between 0 and 0.5 for evaluation.
4The calculator returns JSON with the estimated or selected theta, LOD result, and linkage conclusion, using the requested decimal precision.

Use cases

Teaching Mendelian genetics, recombination fractions, and logarithm-of-odds calculations.
Checking two-point linkage exercises with known recombinant and non-recombinant meiosis counts.
Comparing linkage evidence at an estimated theta versus a fixed genetic distance.

Examples

1. Significant linkage from 2 recombinant meioses

Genetics student

Background

A phase-known sample contains 2 recombinant and 18 non-recombinant meioses, for 20 informative meioses in total.

Problem

Determine the estimated recombination fraction and whether the sample provides significant evidence for linkage.

How to use

Select Maximum LOD, enter 2 recombinant meioses and 18 non-recombinant meioses, and set Decimal Places to 4.

thetaMode: max; recombinantCount: 2; nonRecombinantCount: 18; decimalPlaces: 4

Outcome

The calculator estimates theta-hat = 0.1 and Zmax = 3.197, indicating significant evidence for linkage.

2. Evaluate linkage at a fixed theta

Linkage analysis learner

Background

A sample contains 10 recombinant and 10 non-recombinant meioses, giving a recombinant fraction of 0.5.

Problem

Test whether the data support linkage at theta = 0.1.

How to use

Select Evaluate LOD at fixed theta, enter 10 for both counts, set theta to 0.1, and choose 4 decimal places.

FAQ

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.

thetaMode: fixed; recombinantCount: 10; nonRecombinantCount: 10; theta: 0.1; decimalPlaces: 4

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Learn when to use this tool, what it supports, and how real users apply it.

Key facts

Overview

When to use

How it works

Use cases

Examples

1. Significant linkage from 2 recombinant meioses

2. Evaluate linkage at a fixed theta

FAQ

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