Mitochondrial Region Coverage

Map unioned sequence coverage to caller-defined mitochondrial hypervariable regions.

Description

Coverage of mitochondrial regions should use interval unions so overlapping reads or ranges do not inflate covered bases.

Coverage of mitochondrial regions should use interval unions so overlapping reads or ranges do not inflate covered bases. Each region has its own coverage denominator.

Map unioned sequence coverage to caller-defined mitochondrial hypervariable regions.

When to use Mitochondrial Region Coverage

Use this for the following task: Map unioned sequence coverage to caller-defined mitochondrial hypervariable regions.

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.

How to use Mitochondrial Region Coverage and understand its results

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
Enter regionNames, regionStarts, regionEnds, coveredStarts, coveredEnds using the field table, then run the tool.
Read coveredBases, coveragePercent. Interpret flags, units, ordering and placeholder values using the rules below.
Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.

Input field	Meaning	Value type and bounds	Requirement
regionNames	Region names	list of string; each entry: string	Required
regionStarts	Zero-based half-open interval starts; coverage overlaps are unioned.	list of number; each entry: number	Required
regionEnds	Region ends	list of number; each entry: number	Required
coveredStarts	Covered starts	list of number; each entry: number	Required
coveredEnds	Covered ends	list of number; each entry: number	Required

Supply aligned positive-length zero-based half-open regions and coverage intervals. Sort and merge touching/overlapping coverage, then intersect with each region.^[1]

covered region bases = sum of intersection lengths with unioned coverage; percent = 100 covered/regionLength

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
coveredBases	Covered bases	list of number
coveragePercent	Coverage percent	list of number

json

{
  "input": {
    "regionNames": [
      "HV1",
      "HV2"
    ],
    "regionStarts": [
      0,
      100
    ],
    "regionEnds": [
      50,
      150
    ],
    "coveredStarts": [
      10,
      90
    ],
    "coveredEnds": [
      40,
      160
    ]
  },
  "output": {
    "coveredBases": [
      30,
      50
    ],
    "coveragePercent": [
      60,
      100
    ]
  }
}

Limitations and assumptions

Circular-origin-spanning regions must be represented appropriately by the caller. No mitochondrial reference or fixed hypervariable-region definition is embedded.

The tool evaluates supplied observations or a declared model. It does not establish the biological cause of an observed pattern. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.

Alternative or Complementary methods

Choose BED Intersection for this operation: Intersect two chromosome-aware zero-based half-open BED intervals. For a complementary task, use STR Panel Completeness for this operation: Audit STR panel completeness against a caller-supplied locus set, not an embedded legacy policy.

The implementation reference documents the exact calculation, supported input shapes and returned fields.

References

Mitochondrial Region Coverage — tool.io

Similar or alternative tools

BED Intersection
Intersect two chromosome-aware zero-based half-open BED intervals.
STR Panel Completeness
Audit STR panel completeness against a caller-supplied locus set, not an embedded legacy policy.