On Target Read Efficiency
Compute capture efficiency as the fraction of mapped reads overlapping targets.
Description
Capture efficiency describes the share of mapped reads overlapping intended targets.
Capture efficiency describes the share of mapped reads overlapping intended targets. The denominator must refer to the same read population.
Compute capture efficiency as the fraction of mapped reads overlapping targets.
When to use On Target Read Efficiency
Use this for the following task: Compute capture efficiency as the fraction of mapped reads overlapping targets.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use On Target Read Efficiency and understand its results
- Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
- Enter onTargetReads, totalMappedReads using the field table, then run the tool.
- Read onTargetPercent, offTargetReads. 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 |
|---|---|---|---|
| onTargetReads | On target reads | integer; minimum 0 | Required |
| totalMappedReads | Total mapped reads | integer; minimum 1 | Required |
Require positive mapped total and on-target count between zero and that total. Return on-target percent and off-target count.1
onTargetPercent = 100 onTargetReads/totalMappedReads This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| onTargetPercent | On target percent | number |
| offTargetReads | Off target reads | integer |
{
"input": {
"onTargetReads": 800,
"totalMappedReads": 1000
},
"output": {
"onTargetPercent": 80,
"offTargetReads": 200
}
}Limitations and assumptions
This does not calculate overlap from alignments or establish coverage uniformity.
The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. 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 On Bait Enrichment for this operation: Estimate target enrichment relative to the genomic fraction covered by baits. For a complementary task, use Target Coverage Read Pairs for this operation: Plan paired reads for target coverage from read length and usable on-target pair fraction.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
On Target Read Efficiency — tool.io
Similar or alternative tools
- On Bait Enrichment
Estimate target enrichment relative to the genomic fraction covered by baits.
- Target Coverage Read Pairs
Plan paired reads for target coverage from read length and usable on-target pair fraction.