Multilocus Genotype Match

Calculate theta-adjusted genotype match probabilities and their independent-locus product and log score.

Description

A multilocus random-match model combines per-locus genotype frequencies under an independence assumption.

A multilocus random-match model combines per-locus genotype frequencies under an independence assumption. A theta adjustment modifies homozygous and heterozygous probabilities.

Calculate theta-adjusted genotype match probabilities and their independent-locus product and log score.

When to use Multilocus Genotype Match

Use this for the following task: Calculate theta-adjusted genotype match probabilities and their independent-locus product and log score.

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.

How to use Multilocus Genotype Match and understand its results

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
Enter firstAlleleFrequencies, secondAlleleFrequencies, homozygousFlags, theta using the field table, then run the tool.
Read locusMatchProbabilities, randomMatchProbability, log10MatchProbability. Interpret flags, units, ordering and placeholder values using the rules below.
Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.

Input field	Meaning	Value type and bounds	Requirement
firstAlleleFrequencies	First allele frequencies	list of number; each entry: number	Required
secondAlleleFrequencies	Second allele frequencies	list of number; each entry: number	Required
homozygousFlags	Homozygous flags	list of number; each entry: number	Required
theta	Theta	number	Required

Align positive allele frequencies and numeric 0/1 homozygous flags. Require equal p/q for homozygotes and compatible heterozygous marginals. Compute each probability and preserve the logarithmic score when the product underflows.^[1]

homo: p[θ+(1−θ)p]; hetero: 2(1−θ)pq; log10 product = Σlog10(locusProbability)

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
locusMatchProbabilities	Locus match probabilities	list of number
randomMatchProbability	Random match probability	number
log10MatchProbability	Log 10 match probability	number

json

{
  "input": {
    "firstAlleleFrequencies": [
      0.5,
      0.2
    ],
    "secondAlleleFrequencies": [
      0.5,
      0.3
    ],
    "homozygousFlags": [
      1,
      0
    ],
    "theta": 0
  },
  "output": {
    "locusMatchProbabilities": [
      0.25,
      0.12
    ],
    "randomMatchProbability": 0.029999999999999995,
    "log10MatchProbability": -1.5228787452803376
  }
}

Limitations and assumptions

Zero implied locus probabilities are rejected. The model is not a paternity or identity conclusion, and locus independence/frequency suitability are assumptions.

The tool evaluates supplied observations or a declared model. It does not establish the biological cause of an observed pattern. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.

Alternative or Complementary methods

Choose Exclusion Mismatch Tolerance for this operation: Count exact diploid STR genotype mismatches against a caller-defined tolerance; not a paternity conclusion. For a complementary task, use Signed Dprime for this operation: Normalize signed linkage disequilibrium D by its sign-specific feasible maximum.

The implementation reference documents the exact calculation, supported input shapes and returned fields.

References

Multilocus Genotype Match — tool.io

Similar or alternative tools

Exclusion Mismatch Tolerance
Count exact diploid STR genotype mismatches against a caller-defined tolerance; not a paternity conclusion.
Signed Dprime
Normalize signed linkage disequilibrium D by its sign-specific feasible maximum.