Multi-Mapping Read Ambiguity MAPQ Zero Flag Counter
Count MAPQ zero and unavailable-255 separately; zero MAPQ indicates low confidence, not proof of a unique multi-mapping mechanism.
Description
Count MAPQ zero and unavailable-255 separately; zero MAPQ indicates low confidence, not proof of a unique multi-mapping mechanism.
Mapping-quality flags summarize aligner confidence conventions, which differ from directly proving multimapping. Counting special values preserves those distinctions for a later audit.
When to use this tool
Count MAPQ zero and unavailable-255 separately; zero MAPQ indicates low confidence, not proof of a unique multi-mapping mechanism.
- Prepare the supplied mapqValues fields for this operation.
- Compare the complete example with the representation used by your own input before carrying the result into another step.
How to use the tool and how it works
- Enter mapqValues. Use the exact text syntax, units and index conventions explained below.
- Run the tool. If input validation fails, correct the supplied fields before interpreting any result.
- Read result.zeroMapqCount, result.unavailable255Count, result.multiMappingConfirmed. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.
Require integer mapqValues from zero through 255. Count zeros and 255s separately and return multiMappingConfirmed false.1
| Input field | Meaning and representation | Accepted input |
|---|---|---|
| mapqValues | mapq values. | List of finite numbers; bounded by the operation |
| Output field | Interpretation |
|---|---|
| result | Object containing the named outputs below. |
| result.zeroMapqCount | The zero mapq count value under the stated formula or text convention. |
| result.unavailable255Count | The unavailable255 count value under the stated formula or text convention. |
| result.multiMappingConfirmed | Flag for multi mapping confirmed under the exact condition described above. |
{
"input": {
"mapqValues": [
0,
20,
255,
0
]
},
"output": {
"result": {
"zeroMapqCount": 2,
"unavailable255Count": 1,
"multiMappingConfirmed": false
}
}
}Limitations and assumptions
- No alignment records are read and no mapper-specific probability interpretation is inferred. A zero value alone does not confirm multimapping; 255 is reported separately rather than treated as maximum confidence.
- Every declared top-level field is required and unexpected fields are rejected. Numeric inputs must be finite; ordinary text fields are bounded to 8,192 UTF-16 code units, with tighter operation-specific limits where stated.
- Ordinary string lists have at most 128 entries of at most 128 code units each; numeric lists and matrices have separate bounded size checks. Nonfinite results and excessively large serialized outputs are rejected.
- Indexes are zero-based and spans have an exclusive end unless explicitly stated otherwise. A valid false, null or empty-list result is distinct from malformed input.
Alternative or Complementary methods
Retain the reference assembly, accession/version and measurement convention with an analysis. Length summaries, flags and lookup notes do not validate an assembly or classify a variant; use the corresponding sequence, alignment or evidence-review workflow.
References
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