Transition Transversion Ratio
Classify substitutions as transitions or transversions and compare Ti/Tv with supplied bounds.
Description
Transitions exchange A with G or C with T; other single-base substitutions are transversions.
Transitions exchange A with G or C with T; other single-base substitutions are transversions. Their count ratio can be screened against an appropriate reference range.
Classify substitutions as transitions or transversions and compare Ti/Tv with supplied bounds.
When to use Transition Transversion Ratio
Use this for the following task: Classify substitutions as transitions or transversions and compare Ti/Tv with supplied bounds.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Transition Transversion Ratio 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 referenceBases, alternateBases, minimumRatio, maximumRatio using the field table, then run the tool.
- Read transitions, transversions, titvRatio, 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 |
|---|---|---|---|
| referenceBases | Reference bases | list of string; minimum entries 1; maximum entries 100000; each entry: string; minimum text length 1; maximum text length 1000000; pattern ^\s*[ACGTacgt]\s*$ | Required |
| alternateBases | Alternate bases | list of string; minimum entries 1; maximum entries 100000; each entry: string; minimum text length 1; maximum text length 1000000; pattern ^\s*[ACGTacgt]\s*$ | Required |
| minimumRatio | Minimum ratio | number; minimum 0 | Required |
| maximumRatio | Maximum ratio | number; minimum 0 | Required |
Align canonical single-base references and alternates, normalize case/outer whitespace and reject identical pairs. Require at least one transversion and compare the ratio with inclusive supplied bounds.1
Ti/Tv = transitionCount/transversionCount This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| transitions | Transitions | integer |
| transversions | Transversions | integer |
| titvRatio | Titv ratio | number |
| withinRange | Within range | boolean |
{
"input": {
"referenceBases": [
"A",
"C",
"A",
"G"
],
"alternateBases": [
"G",
"T",
"C",
"T"
],
"minimumRatio": 0.5,
"maximumRatio": 2
},
"output": {
"transitions": 2,
"transversions": 2,
"titvRatio": 1,
"withinRange": true
}
}Limitations and assumptions
A transition-only set has an undefined finite ratio and produces an input error. Passing a range does not establish variant quality.
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 Het Hom Ratio Screen for this operation: Screen heterozygous/homozygous-alternate variant ratio against caller-supplied cohort expectations. For a complementary task, use Mutation Context 96 Index for this operation: Index 96 pyrimidine-oriented mutation channels in substitution-major then A/C/G/T flank order.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Transition Transversion Ratio — tool.io
Similar or alternative tools
- Het Hom Ratio Screen
Screen heterozygous/homozygous-alternate variant ratio against caller-supplied cohort expectations.
- Mutation Context 96 Index
Index 96 pyrimidine-oriented mutation channels in substitution-major then A/C/G/T flank order.