Recombination Frequency Calculator
Work out recombination frequency from test-cross counts, an F2 [ab] proportion, or a gamete ratio. The tool identifies the parental and recombinant classes, distinguishes coupling from repulsion, and shows the working so you can check genetics problems step by step.
Offspring counts by phenotype from a cross with aabb (test cross)
Assumes selfing or a cross between identical genotypes
Enter a total to also show expected counts
Try an example
Choose a pattern and enter counts or a ratio.
How to use
- 1
Pick a pattern
Choose test-cross counts, an F2 [ab] proportion, or a gamete ratio from a known recombination frequency.
- 2
Enter counts or a ratio
For a test cross enter the four phenotype counts; for F2 enter the total and the [ab] count; for gametes enter the frequency and phase.
- 3
Check the working and verdict
See the parental and recombinant classes, the calculation, and whether the genes are completely linked, incompletely linked, or independent.
Features
- Finds the parental and recombinant classes from four test-cross counts
- Infers coupling or repulsion from an F2 [ab] proportion and back-calculates RF
- Turns an RF into the gamete ratio n:1:1:n with expected counts
- Reports complete linkage, incomplete linkage or independence, plus the map-distance guide
- Runs entirely in your browser; no sign-up and nothing uploaded
Use cases
Check homework
Verify test-cross and F2 problems from the parental/recombinant classification onward.
Exam practice
See the working for common mistakes such as swapping coupling and repulsion or using the wrong denominator.
Prepare a genetic map
Convert RF into a map-distance guide (1% = 1 cM) for three-point cross work.
Details
Recombination frequency (RF) is the proportion of recombinant gametes produced by crossing over between two linked genes. It is recombinant gametes ÷ total gametes × 100. An RF of 0% means complete linkage, between 0% and 50% incomplete linkage, and 50% independence. Because crossing over occurs only between homologous chromosomes, RF cannot exceed 50% by definition.
In a test cross (a cross with aabb), the other parent contributes only ab gametes, so the offspring phenotype ratio directly reflects the F1 gamete ratio. The two larger classes are parental and the two smaller classes are recombinant. If the parental pair is AB and ab, the phase is coupling (AB/ab); if it is Ab and aB, the phase is repulsion (Ab/aB). The denominator of RF is the total, not just the parental classes. If parental or recombinant counts are unequal, or the parental pair is neither coupling nor repulsion, check sampling variation and phenotype scoring.
From the F2 double-recessive [aabb] proportion q, the phase follows automatically. If q is below 1/16, the phase is repulsion and ab is recombinant; if q is above 1/16, the phase is coupling and ab is parental. Coupling gives q = ((1−r)/2)², so r = 1 − 2√q; repulsion gives q = (r/2)², so r = 2√q. At q = 1/16 the genes are independent (r = 50%). This reverse calculation assumes selfing or identical genotypes, equal recombination in both sexes, complete dominance, and no viability or fertility differences. An RF of 1% is used as 1 cM on a genetic map, but it does not always scale with physical distance.
FAQ
How do I tell parental and recombinant classes apart?
In a test cross, the two larger offspring classes are parental and the two smaller are recombinant. RF = (sum of the two smaller classes) ÷ total × 100. Never use only the parental classes as the denominator.
What is the difference between coupling and repulsion?
Coupling means AB and ab are linked on the same chromosome (AB/ab); repulsion means Ab and aB are linked (Ab/aB). In a test cross, parental classes AB and ab indicate coupling, while Ab and aB indicate repulsion. In F2, an [ab] proportion below 1/16 indicates repulsion.
When back-calculating from F2, should I use 1−2√q or 2√q?
If the [ab] proportion q is above 1/16 (= 0.0625), the phase is coupling and r = 1 − 2√q. If q is below 1/16, the phase is repulsion and r = 2√q. At q = 1/16 the genes are independent (r = 50%).
When is recombination frequency 50%?
When the two genes are on different chromosomes, or far apart on the same chromosome. The gamete ratio approaches 1:1:1:1 regardless of crossing over, so linkage cannot be concluded.
What if the observed counts are not equal as theory predicts?
Parental counts should be nearly equal, and recombinant counts too. Large gaps may come from sampling variation, differences in viability or fertility, or phenotype scoring errors. This tool still calculates from the totals and shows a note.
All processing happens in your browser. Your files are never uploaded.
Verified: Textbook cases (test cross 9:1:1:9 giving 10%, 1:4:4:1 giving 20%, complete linkage 0%, independence 50%, F2 [ab] 0.16 giving 20% and 0.01 giving 20%, and RF 20% giving the gamete ratio 4:1:1:4) plus error handling are covered by browser tests
Did you know?
Recombination frequency never exceeds 50% by definition. Even on the same chromosome, genes far apart approach 50% and become indistinguishable from independence. A frequency of 1% is used as 1 cM on a genetic map.