Output DBS

Output - DBS (Double Base Substitution)

This page provides detailed information about Double Base Substitution (DBS) output files.

Overview

DBS matrices classify dinucleotide variants where two adjacent bases are mutated simultaneously.

Output Files

File	# of Sequences	Description
test.DBS78.all	78	Pyrimidine dinucleotide variants
test.DBS186.all	186	78 + TSB categories
test.DBS1248.all	1248	With flanking nucleotide context
test.DBS2976.all	2976	Extended context + TSB

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DBS-78

The DBS78 file contains the frequency of pyrimidine double nucleotide variants.

Dinucleotide Combinations

Only the 10 dinucleotide combinations with the highest pyrimidine content are considered:

• AC, AT, CC, CG, CT, GC, TA, TC, TG, TT

Mutation Possibilities

• 4 combinations (CG, GC, AT, TA) have 6 possible mutations each
• 6 combinations have 9 possible mutations each

Calculation: (6 × 4) + (9 × 6) = 24 + 54 = 78 combinations

Example: Line listing AC>CG shows the frequency of AC to CG mutations across all samples.

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DBS-186

DBS-186 extends DBS-78 by incorporating transcriptional strand bias categories.

Pyrimidine-only Dinucleotides

The 4 dinucleotide combinations consisting only of pyrimidines (CT, TC, CC, TT) are categorized into:

Category	Description
T	Transcribed strand
U	Untranscribed strand
N	Non-transcribed
B	Bidirectional
Q	Questionable (for other combinations)

Calculation:

• 36 sequences × 4 categories = 144
• Plus questionable categories = 186 total

Example: T:AC>GA indicates an AC sequence on the transcribed strand mutating to GA.

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DBS-1248

DBS-1248 adds flanking nucleotide context to DBS-78.

Format: N[XY>ZW]N

Where N represents any nucleotide at the 5' or 3' position.

Calculation: 4 (5' nucleotide) × 78 × 4 (3' nucleotide) = 1248 combinations

Example: A[AC>CG]C corresponds to AACC sequences mutating to ACGC.

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DBS-2976

DBS-2976 extends DBS-186 with flanking nucleotide context.

Calculation: 4 × 186 × 4 = 2976 combinations

Example: T:A[AC>CG]T corresponds to AACT on the transcribed strand mutating to ACGT.

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File Extensions

Extension	Description
.all	All mutations (default)
.exome	Mutations mapped to exome regions
.region	Mutations mapped to custom BED file regions
.chrX	Chromosome-specific mutations