Source: https://guthlabs.ai/docs/instruments/allele-genotype-frequency-from-pedigree-counts/

instrument / verified-clean

# Allele/Genotype Frequency from Pedigree Counts

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

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

## Inspectable records

[01**Overview**Purpose and lifecycle](<https://guthlabs.ai/docs/instruments/allele-genotype-frequency-from-pedigree-counts/>)[02**Mechanism**Method and assumptions](<https://guthlabs.ai/docs/instruments/allele-genotype-frequency-from-pedigree-counts/mechanism/>)[03**Implementation**Binding and validation](<https://guthlabs.ai/docs/instruments/allele-genotype-frequency-from-pedigree-counts/implementation/>)[04**Qualification**Evidence and errata](<https://guthlabs.ai/docs/instruments/allele-genotype-frequency-from-pedigree-counts/qualification/>)

## 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**: t5-133

**Ledger rows**: 1

No ledger note is attached.

## Review findings

The allele-frequency formulas are conditionally correct, but the specification is incomplete and ambiguous because it omits the HWE expected-count formulas and does not define the required constraints on N and genotype counts. Retain the educational/not-medical-advice label, and explicitly state that this is not a clinical, diagnostic, or population-inference result.

### Formula and scope findings

- The allele-frequency formula p=(2×AA+Aa)/(2N) is standard only when N is the total number of individuals and AA, Aa, and aa are mutually exclusive, exhaustive genotype counts at a biallelic locus.

- q=1−p is standard under the same biallelic-locus assumption; otherwise q should be computed from the allele count for the alternate allele.

- The specification claims to output expected HWE genotype counts but does not provide formulas. The required standard formulas are expected_AA=Np², expected_Aa=2Npq, and expected_aa=Nq².

- The phrase 'codominant/recessive' is ambiguous: raw genotype counts support this calculation, but recessive phenotype counts alone do not identify AA versus Aa without additional assumptions or data.

- Pedigree-derived counts are not automatically population-genetic random-sample counts, so HWE expected counts require an explicit idealized random-mating/population-sampling assumption.

### Unit assumptions

- AA, Aa, and aa are nonnegative integer counts of individuals, not percentages or frequencies.

- N is the total individual count and must equal AA+Aa+aa.

- The locus is biallelic, with no missing, ambiguous, or additional alleles/genotypes.

- p denotes the frequency of the A allele and q denotes the frequency of the a allele.

- Expected HWE outputs are counts of individuals; p and q are dimensionless proportions.

- HWE expected counts assume random mating and the stated idealized population assumptions.

## Boundary hardening

**BREAK_CLAIMED** · SELF_FLAGGED

The N=0 vector produces a 0/0 division and all downstream outputs are undefined; the instrument must reject it. The convention probe also exposes an unvalidated mismatch between supplied N and the sum of genotype counts.

## 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": {
    "AA": 36,
    "Aa": 48,
    "aa": 16,
    "N": 100
  },
  "expected_outputs": {
    "p": 0.6,
    "q": 0.4,
    "expected_AA": 36,
    "expected_Aa": 48,
    "expected_aa": 16
  },
  "working": "Check N: 36+48+16=100. A-allele count = 2×36+48=72+48=120. Total allele count = 2×100=200. p=120/200=0.6. q=1−0.6=0.4. HWE expected_AA=100×0.6²=100×0.36=36. expected_Aa=2×100×0.6×0.4=200×0.24=48. expected_aa=100×0.4²=100×0.16=16."
}
````

## 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`