Source: https://guthlabs.ai/docs/instruments/genetic-linkage-recombination-frequency-calculator/mechanism/

instrument mechanism / verified-clean

# Genetic Linkage / Recombination Frequency Calculator mechanism

The inspectable method record for Genetic Linkage / Recombination Frequency Calculator, kept separate from implementation and qualification.

Status: **VERIFIED_CLEAN**Lifecycle: **verified-clean**

## Model scope

The RF percentage calculation is valid, but the unqualified claim that it equals map distance in cM is not generally correct. Keep the educational label, add strict input validation, and rename the second output to something such as "RF-based approximate distance (cM)" unless a specified mapping function and its assumptions are implemented.

- RF=(recombinant count/total offspring count)×100 is the standard observed recombination-frequency percentage, provided counts are valid and the denominator is nonzero.

- Equating recombination frequency percentage directly with map distance in cM is only a small-distance approximation. Recombination fraction saturates at 50%, whereas genetic map distance can exceed 50 cM because of multiple crossovers.

- For larger distances, a mapping function such as Haldane d=-50×ln(1-2r) cM or Kosambi d=25×ln((1+2r)/(1-2r)) cM is needed, with explicit assumptions. Here r is the fraction recombinant, not the percentage.

- The specification does not state whether the reported cM value is intentionally the classical RF-percent approximation or a mapping-function distance; the output label should not imply an exact map distance.

## Units and conventions

- Recombinant count and total offspring count are nonnegative integer counts of offspring from the same cross.

- RF as a fraction is recombinant count divided by total offspring count; RF percentage is that fraction multiplied by 100.

- The naive RF-percent-to-cM conversion treats 1 percentage point of RF as approximately 1 cM and is defensible only for sufficiently small separations.

- Counts are dimensionless; RF is a fraction or percentage, and map distance is expressed in cM.

- Total offspring count must be greater than zero.

- Recombinant count must not exceed total offspring count; for a standard two-point testcross, the observable recombinant fraction is at most 0.5.

## Inspectable vector

One of 4 source-bound review vectors:

````
{
  "inputs": {
    "recombinant_count": 37,
    "total_offspring_count": 412
  },
  "expected_outputs": {
    "recombination_frequency_percent": 8.9805825243,
    "map_distance_cM_RF_approximation": 8.9805825243
  },
  "working": "RF fraction = 37 ÷ 412 = 0.089805825243...; RF percent = 0.089805825243... × 100 = 8.9805825243...%; naive RF-based map distance = 8.9805825243... cM."
}
````

## Failure boundary

**BREAK_CLAIMED** · SELF_FLAGGED

The specification has a definite undefined-result trap when total_offspring=0. It also permits plain arithmetic above the classical 50% two-point mapping limit unless the instrument separately validates or warns, producing a formally computable but biologically invalid classical estimate.

## Other records

[01**Overview**](<https://guthlabs.ai/docs/instruments/genetic-linkage-recombination-frequency-calculator/>)[03**Implementation**](<https://guthlabs.ai/docs/instruments/genetic-linkage-recombination-frequency-calculator/implementation/>)[04**Qualification**](<https://guthlabs.ai/docs/instruments/genetic-linkage-recombination-frequency-calculator/qualification/>)

## Sources and evidence

These pointers bind the page to evidence. They do not grant authority or collapse verification into deployment.

- `VERIFIED_LEDGER.json`

- `evidence-tranche5/tranche5-results.json`

- `BOUNDARY_HAZARD_CATALOG.json`