Description
For nonnegative integer expected, calledCopies, and unknownCopies return knownGap=calledCopies-expected, possibleMinimum=calledCopies, possibleMaximum=calledCopies+unknownCopies, and definitelyMismatch when expected lies outside that interval.
Pharmacogenomic records distinguish allele labels, copy counts, reference-sequence versions, coordinate systems, and evidence about chromosome phase. A balanced count or matching token can check a record without establishing the underlying genotype. Supplied activity values and interpretation rules remain separate from a current gene-specific clinical guideline.
For nonnegative integer expected, calledCopies, and unknownCopies return knownGap=calledCopies-expected, possibleMinimum=calledCopies, possibleMaximum=calledCopies+unknownCopies, and definitelyMismatch when expected lies outside that interval.
When to use this tool
Use Pharmacogenomic Sample Ploidy Mismatch when you need this specific allele-token, reference-coordinate, copy-budget, or source-support check.
How to use the tool and how it works
- Enter expected, calledCopies, unknownCopies. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read knownGap, possibleMinimum, possibleMaximum, definitelyMismatch. Inspect definitelyMismatch before interpreting the associated values.
For nonnegative integer expected, calledCopies, and unknownCopies return knownGap=calledCopies-expected, possibleMinimum=calledCopies, possibleMaximum=calledCopies+unknownCopies, and definitelyMismatch when expected lies outside that interval.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| expected | Expected | Required. Safe integer; minimum 0. |
| calledCopies | Called Copies | Required. Safe integer; minimum 0. |
| unknownCopies | Unknown Copies | Required. Safe integer; minimum 0. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| knownGap | Known Gap | Required. Safe integer. |
| possibleMinimum | Possible Minimum | Required. Safe integer. |
| possibleMaximum | Possible Maximum | Required. Safe integer. |
| definitelyMismatch | Definitely Mismatch | Required. Boolean. |
{
"input": {
"expected": 2,
"calledCopies": 1,
"unknownCopies": 1
},
"output": {
"knownGap": -1,
"possibleMinimum": 1,
"possibleMaximum": 2,
"definitelyMismatch": false
}
}Limitations and assumptions
- UnknownCopies is a supplied upper-budget contribution, not a probabilistic uncertainty estimate. An expected count inside the range does not establish a correct ploidy or validated genotype.
- 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. Signed zero is exported as zero.
Alternative or Complementary methods
Use a current gene-specific nomenclature and a validated interpretation process when allele identity, phase, function, or clinical decisions matter. Verify source versions and reference coordinates before combining records.
References
Similar or alternative tools
- Pharmacogenomic Assay Covered Variant Check
Audit explicitly supplied assay-coverage IDs without predicting assay sensitivity.
- Pharmacogenomic Assembly Coordinate Source Pair
Compare supplied coordinate/reference metadata without liftover or sequence interpretation.