Description
Calculate allele frequency using callable alleles and report missing possible alleles.
Evolutionary summaries depend on sampled sequences/populations, reference states, ploidy, time units and stochastic assumptions. A mixture expectation differs from a drift simulation, and a callable-allele denominator differs from an individual count. Labels and local tree conditions do not reconstruct ancestry or establish a biological mechanism.
Calculate allele frequency using callable alleles and report missing possible alleles.
When to use this tool
Use Allele Count Ploidy Denominator Label when checking the stated evolutionary record, reference, expectation or scale convention.
How to use the tool and how it works
- Enter sampledIndividuals, ploidy, callableAlleles, alleleCount. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read possibleAlleles, missingAlleles, observedFrequency, defined. Inspect defined before interpreting the associated values.
Require whole sampledIndividuals>=0, ploidy>=1, callableAlleles within individuals*ploidy and alleleCount within callable. Return nominal possible alleles, possible-callable missing alleles and alleleCount/callable, or zero with defined=false when callable=0.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| sampledIndividuals | Sampled Individuals | Required. Safe integer; minimum 0. |
| ploidy | Ploidy | Required. Safe integer; minimum 1. |
| callableAlleles | Callable Alleles | Required. Safe integer; minimum 0. |
| alleleCount | Allele Count | Required. Safe integer; minimum 0. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| possibleAlleles | Numeric sampledIndividuals*ploidy product; not arbitrary-precision integer text. | Required. Safe integer. |
| missingAlleles | Missing Alleles | Required. Safe integer. |
| observedFrequency | alleleCount/callableAlleles, or zero placeholder when defined=false. | Required. Finite number. |
| defined | Whether the corresponding reporting denominator/direction is defined; inspect before interpreting zero placeholders. | Required. Boolean. |
{
"input": {
"sampledIndividuals": 10,
"ploidy": 2,
"callableAlleles": 18,
"alleleCount": 6
},
"output": {
"possibleAlleles": 20,
"missingAlleles": 2,
"observedFrequency": 0.3333333333333333,
"defined": true
}
}Limitations and assumptions
- Frequency uses callable alleles rather than individuals; nominal count products are numeric, not arbitrary-precision text, and no variant calling or ploidy inference occurs.
- Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.
- Numeric calculations use binary floating point unless exact decimal-integer arithmetic is explicitly stated. No hidden measurement tolerance or decimal rounding is added; nonfinite or out-of-contract results are rejected. Numeric signed-zero results are exported as zero.
Alternative or Complementary methods
Use verified samples/references and appropriate complete phylogenetic, population-genetic or statistical models for actual biological inference and uncertainty.
References
Similar or alternative tools
- Population Transfer Dilution Count
Calculate expected transferred and remaining population counts under a supplied transfer fraction.
- Migration Drift Generation Expectation
Calculate an expected allele frequency after deterministic migration mixing.