Consensus Sequence Coverage Percent Depth Calculator
Summarize supplied per-base consensus depth and coverage threshold; does not align reads or generate a consensus sequence.
Description
Summarize supplied per-base consensus depth and coverage threshold; does not align reads or generate a consensus sequence.
Coverage breadth and mean depth describe different aspects of a supplied per-base depth vector. A depth threshold makes the breadth calculation explicit.
When to use this tool
Summarize supplied per-base consensus depth and coverage threshold; does not align reads or generate a consensus sequence.
- Prepare the supplied depths, minimumDepth 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 depths, minimumDepth. 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.coveredBaseCount, result.coveredPercent, result.meanDepth. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.
Require nonempty depths of nonnegative integers up to one billion and an integer minimumDepth from one through one billion. Count entries at or above the threshold, divide by the number of entries for coveredPercent, and return their arithmetic mean as meanDepth.1
| Input field | Meaning and representation | Accepted input |
|---|---|---|
| depths | depths. | List of finite numbers; bounded by the operation |
| minimumDepth | minimum depth. | Integer from 1 to 1e9 inclusive |
| Output field | Interpretation |
|---|---|
| result | Object containing the named outputs below. |
| result.coveredBaseCount | The covered base count value under the stated formula or text convention. |
| result.coveredPercent | The covered percent value under the stated formula or text convention. |
| result.meanDepth | The mean depth value under the stated formula or text convention. |
{
"input": {
"depths": [
0,
10,
20,
30
],
"minimumDepth": 10
},
"output": {
"result": {
"coveredBaseCount": 3,
"coveredPercent": 75,
"meanDepth": 15
}
}
}Limitations and assumptions
- The vector must already represent the intended full reference span. The tool does not align reads, account for missing unlisted positions, call a consensus or establish sequence accuracy.
- 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
Keep physical-particle counts, infectious assay units and observed sample proportions distinct. Use the original calibration, product instructions or validated assay method for the specific context; simple conversions and reference notes do not establish infectivity or clinical interpretation.
References
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