Recombination frequency (%RF) calculator
Recombination frequency (RF) measures how often a crossover event produces recombinant allele
combinations between two loci during meiosis. In a two-gene testcross, RF is estimated directly from offspring
counts by comparing the number of recombinant offspring to the total offspring.
When to use %RF
RF is most commonly computed from a testcross:
a heterozygote for two genes crossed with a double-recessive tester (ab/ab).
Because the tester produces only ab gametes, the offspring classes reflect the gametes produced by the
heterozygous parent, making it easy to identify parental vs recombinant types.
\[
\text{Testcross:}\quad \text{(heterozygote)} \times \frac{ab}{ab}
\]
Key idea: parental vs recombinant classes
In a two-locus testcross there are four possible offspring classes: AB, ab, Ab, aB.
Typically, two classes are parental (non-recombinant) and two are recombinant.
Recombinant classes arise when crossing over occurs between the loci.
Coupling vs repulsion phase
Which offspring classes count as recombinant depends on the phase (how alleles are arranged on the homologous
chromosomes in the heterozygous parent).
\[
\text{Coupling (cis):}\ \frac{AB}{ab}
\qquad\qquad
\text{Repulsion (trans):}\ \frac{Ab}{aB}
\]
Under coupling (AB/ab), the parental types are AB and ab, so the recombinants are
Ab and aB.
Under repulsion (Ab/aB), the parental types are Ab and aB, so the recombinants are
AB and ab.
\[
\text{Coupling: recombinants } = Ab,\ aB
\]
\[
\text{Repulsion: recombinants } = AB,\ ab
\]
Step-by-step formula for recombination frequency
Let R be the total number of recombinant offspring and N be the total offspring count across all four
classes. The recombination frequency is the recombinant fraction expressed as a percent.
\[
N = AB + ab + Ab + aB
\]
\[
R = \text{(sum of the two recombinant classes)}
\]
\[
\%RF = 100\cdot\frac{R}{N}
\]
Interpreting %RF (simple linkage conclusion)
In the standard two-locus model, RF is bounded between 0% and 50%.
Smaller values indicate stronger linkage because most gametes remain parental.
Values near 50% indicate behavior similar to independent assortment.
\[
0\% \le \%RF \le 50\%
\]
Practical rule of thumb used in this calculator:
%RF < 50% suggests the genes are linked (at least to some extent),
while %RF \approx 50% suggests the genes are effectively unlinked / assort independently.
If your computed value is above 50%, the most common cause is that the recombinant classes were labeled
incorrectly (for example, swapping parental and recombinant classes).
Why the visualizations help
The donut chart summarizes the split between parental and recombinant offspring.
The four-bar chart shows which two classes dominate (often the parental classes when linkage is present).
The RF gauge places the computed %RF on a 0–50% scale so you can quickly see whether the result is closer to
tight linkage (near 0%) or independent behavior (near 50%).
Notes and limitations
This calculator provides a descriptive estimate of recombination frequency and a simple linkage interpretation.
It does not run a statistical test (such as a chi-square goodness-of-fit test) and does not compute map distance
corrections for multiple crossovers. For introductory genetics, %RF is a strong first summary of linkage strength.
Recent reviews
The calculator functions quite well with data, and its interface is both intuitive and aesthetically pleasing. A full 5/5!