Mutation Context 96 Index

Index 96 pyrimidine-oriented mutation channels in substitution-major then A/C/G/T flank order.

Description

Single-base substitution channels combine a mutation type with its flanking bases.

Single-base substitution channels combine a mutation type with its flanking bases. Pyrimidine orientation unifies reverse-complement representations.^[1]

Index 96 pyrimidine-oriented mutation channels in substitution-major then A/C/G/T flank order.

When to use Mutation Context 96 Index

Use this for the following task: Index 96 pyrimidine-oriented mutation channels in substitution-major then A/C/G/T flank order.

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.

How to use Mutation Context 96 Index 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 trinucleotide, alternateBase using the field table, then run the tool.
Read canonicalContext, canonicalChange, channelIndex. 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
trinucleotide	Trinucleotide	string; minimum text length 1; maximum text length 1000000; pattern ^\s[ACGTacgt]{3}\s$	Required
alternateBase	Alternate base	string; minimum text length 1; maximum text length 1000000; pattern ^\s[ACGTacgt]\s$	Required

Require three canonical context bases and a different single alternate. Reverse-complement purine-centered contexts, then use C>A,C>G,C>T,T>A,T>C,T>G and A,C,G,T flank order for index 0–95.^[2]

index = substitutionTypeIndex×16 + leftBaseIndex×4 + rightBaseIndex

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

Output field	Meaning	Value type
canonicalContext	Canonical context	string
canonicalChange	Canonical change	string
channelIndex	Zero-based substitution-major index: C>A, C>G, C>T, T>A, T>C, T>G; then 5-prime and 3-prime bases in A,C,G,T order.	integer

json

{
  "input": {
    "trinucleotide": "ACA",
    "alternateBase": "T"
  },
  "output": {
    "canonicalContext": "ACA",
    "canonicalChange": "C>T",
    "channelIndex": 32
  }
}

Limitations and assumptions

The index order is this tool’s declared convention. It does not fit signatures or infer a mutational cause.

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 Transition Transversion Ratio for this operation: Classify substitutions as transitions or transversions and compare Ti/Tv with supplied bounds. For a complementary task, use Sliding GC Content for this operation: Calculate GC content in complete DNA windows at a chosen step size.

Further background: Background specification: Mutation Context 96 Index.

References

Background specification: Mutation Context 96 Index — cancer.sanger.ac.uk
Mutation Context 96 Index — tool.io

Similar or alternative tools

Transition Transversion Ratio
Classify substitutions as transitions or transversions and compare Ti/Tv with supplied bounds.
Sliding GC Content
Calculate GC content in complete DNA windows at a chosen step size.