Genetic Linkage / Recombination Frequency Calculator

Inspectable records

Ledger state

The current ledger marks this instrument verified clean within the source-bound verification corpus.

Area

Biology, Medicine & Pharmacology (educational estimates only — every panel labeled not-medical-advice)

Tranche

tranche-5

Evidence ID

t5-125

Ledger rows

1

No ledger note is attached.

Review findings

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.

Formula and scope findings

• 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.

Unit assumptions

• 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.

Boundary hardening

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.

Errata and corrections

No applied erratum is attached to this unique-name record.

Inspectable example

4 review vectors are recorded. One source-bound sample is shown below.

{
  "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."
}

Related workflows

No source-defined multi-instrument workflow membership is recorded.

Sources and evidence

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

• VERIFIED_LEDGER.json · VERIFIED_CLEAN
• evidence-tranche5/tranche5-results.json
• BOUNDARY_HAZARD_CATALOG.json