What is a centimorgan (cM)?

One centimorgan (cM), also called one map unit (mu), corresponds to a 1% recombination frequency between two loci. It is named after Thomas Hunt Morgan. Because double crossovers can cancel each other out, map distances above ~50 cM are unreliable estimates of physical distance.

What is the maximum map distance this tool can report?

The recombination frequency between two loci on the same chromosome cannot exceed 50% (0.50), which equals 50 cM. At that point genes assort independently, just like unlinked genes on different chromosomes. If the calculator returns a value close to 50 cM, the loci may be far apart or on different chromosomes.

How do I identify parental vs. recombinant classes in a two-point cross?

Parental classes are the two most frequent phenotype groups — they match the original parental genotypes. Recombinant classes are the two less frequent groups produced by a crossover between the two loci during meiosis.

What is the coefficient of coincidence (CoC)?

The coefficient of coincidence compares the observed double-crossover frequency to the expected frequency (product of the two single-crossover frequencies). A CoC of 1 means crossovers occur independently; a CoC less than 1 indicates positive interference (one crossover inhibits a nearby crossover).

What is interference?

Interference = 1 − CoC. Positive interference (I > 0, CoC 1) means a first crossover increases the probability of another, which is rare.

How do I determine gene order in a three-point cross?

The double-crossover classes are usually the two least frequent phenotype classes. Compare them to the parentals: whichever gene changes relative to the parental combinations is the middle gene. Determine that order first, then enter the classes in the calculator's designated A–B–C slots.

Genetic Map Distance Calculator

Enter offspring counts from a testcross to calculate recombination frequency and genetic map distance in centimorgans (cM).

Cross Type

Testcross Type

Two-point Three-point

Enter offspring counts for each phenotype class. The two most frequent classes are parental; the two least frequent are recombinant.

Parental class 1

Parental class 2

Recombinant class 1

Recombinant class 2

Quick Reference

Map distance (cM) RF × 100

Recombination freq (RF) Recombinants / Total

Coefficient of coincidence Obs DCO / Exp DCO

Interference 1 − CoC

Enter offspring counts and click Calculate Map Distance to see results.

Map Distance

—

centimorgans (cM)

Recombination Freq

—

proportion (0 – 0.5)

Total Offspring

—

Parentals

—

Recombinants

—

Interval Map Distances

Interval	Recombinants	RF	cM

Coeff. of Coincidence

—

Interference

—

DCO observed / expected

Class Breakdown

Class	Count	% of Total	Type

Interpretation

Summary

Genetic mapping distance measures how far apart two genes are on a chromosome, expressed in centimorgans (cM) or map units. One centimorgan equals a 1% recombination frequency — meaning 1 in 100 offspring result from a crossover between the two loci. This calculator takes parental and recombinant class counts from a two-point or three-point testcross and computes recombination frequency, map distance, and coefficient of coincidence (for three-point crosses).

How it works

Select whether you are performing a two-point or three-point testcross.
Enter the observed offspring counts for each phenotype class from your cross.
The tool identifies parental and recombinant classes based on the cross type.
Recombination frequency is calculated as recombinants divided by total offspring.
Map distance in centimorgans equals the recombination frequency multiplied by 100.
For three-point crosses, the tool also calculates the coefficient of coincidence and interference.

Use cases

Convert recombination frequency percentages to centimorgan map distances.
Analyze two-point testcross data to determine gene-to-gene distance.
Construct a three-point linkage map from a three-point testcross.
Calculate the coefficient of coincidence and interference for three loci.
Determine gene order from double-crossover classes in three-point crosses.
Verify whether two genes are linked or assort independently (50 cM threshold).
Solve genetics homework problems involving map distances.
Compare observed and expected double-crossover frequencies.

Frequently Asked Questions

Last updated: 2026-09-30 · Reviewed by Nham Vu