Per Base Generation Mutation Rate
Normalize mutation observations by assayed base-generations and compare with caller-defined bounds.
Description
A per-base per-generation mutation rate normalizes observed events by the genomic territory and generations assayed.
A per-base per-generation mutation rate normalizes observed events by the genomic territory and generations assayed. Numerator and exposure need consistent definitions.
Normalize mutation observations by assayed base-generations and compare with caller-defined bounds.
When to use Per Base Generation Mutation Rate
Use this for the following task: Normalize mutation observations by assayed base-generations and compare with caller-defined bounds.
Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
How to use Per Base Generation Mutation Rate and understand its results
- Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
- Enter newMutations, assayedBases, generations, minimumRate, maximumRate using the field table, then run the tool.
- Read mutationsPerBasePerGeneration, withinRange. 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 |
|---|---|---|---|
| newMutations | New mutations | integer | Required |
| assayedBases | Assayed bases | integer | Required |
| generations | Generations | integer | Required |
| minimumRate | Minimum rate | number | Required |
| maximumRate | Maximum rate | number | Required |
Use nonnegative integer events and positive base/generation counts, with ordered nonnegative reference bounds. Calculate the rate and compare inclusively.1
rate = newMutations/(assayedBases×generations) This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| mutationsPerBasePerGeneration | Mutations per base per generation | number |
| withinRange | Within range | boolean |
{
"input": {
"newMutations": 10,
"assayedBases": 1000,
"generations": 2,
"minimumRate": 0.001,
"maximumRate": 0.01
},
"output": {
"mutationsPerBasePerGeneration": 0.005,
"withinRange": true
}
}Limitations and assumptions
Mutation identification, ascertainment and uncertainty are external. This does not determine whether the supplied observations are independent.
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 Synonymous Clock Divergence for this operation: Estimate divergence time from dS assuming equal constant substitution rates on both lineages. For a complementary task, use Indel Density for this operation: Compute insertion-plus-deletion variant density per callable kilobase.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Per Base Generation Mutation Rate — tool.io
Similar or alternative tools
- Synonymous Clock Divergence
Estimate divergence time from dS assuming equal constant substitution rates on both lineages.
- Indel Density
Compute insertion-plus-deletion variant density per callable kilobase.