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.

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

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

Only the 10 dinucleotide combinations with the highest pyrimidine content are considered: - AC, AT, CC, CG, CT, GC, TA, TC, TG, TT

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.

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

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.

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.

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.

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