Per-Base Sequence Quality Box Stats Summary Note Generator
Summarize supplied per-base Phred scores with type-7 interpolated quartiles; no FASTQ reader or sequencing-run quality verdict.
Description
Summarize supplied per-base Phred scores with type-7 interpolated quartiles; no FASTQ reader or sequencing-run quality verdict.
A five-number quality summary describes the spread of supplied observations. Quartile interpolation needs an explicit convention when a quantile falls between sample positions.
When to use this tool
Summarize supplied per-base Phred scores with type-7 interpolated quartiles; no FASTQ reader or sequencing-run quality verdict.
- Prepare the supplied qualityScores 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 qualityScores. 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.minimum, result.q1, result.median, result.q3, result.maximum. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.
Require a nonempty nonnegative qualityScores list, sort it numerically, and return minimum, q1, median, q3 and maximum. Quantiles use linear interpolation at (n-1)*p between neighboring ordered values.1
| Input field | Meaning and representation | Accepted input |
|---|---|---|
| qualityScores | quality scores. | List of finite numbers; bounded by the operation |
| Output field | Interpretation |
|---|---|
| result | Object containing the named outputs below. |
| result.minimum | The minimum value under the stated formula or text convention. |
| result.q1 | The q1 value under the stated formula or text convention. |
| result.median | The median value under the stated formula or text convention. |
| result.q3 | The q3 value under the stated formula or text convention. |
| result.maximum | The maximum value under the stated formula or text convention. |
{
"input": {
"qualityScores": [
10,
20,
30,
40,
50
]
},
"output": {
"result": {
"minimum": 10,
"q1": 20,
"median": 30,
"q3": 40,
"maximum": 50
}
}
}Limitations and assumptions
- The tool summarizes the supplied vector only; it does not read FASTQ, aggregate cycles across a run or diagnose sequencing failures. Quartiles can be fractional even for integer input scores.
- 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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