Single Base Substitution (SBS)

- Using the Tool - Output

Overview

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Classification of single base substitutions (SBSs). The complete classification of an SBS includes both bases in the Watson-Crick base-pairing. To simplify this notation, one can use either the purine or the pyrimidine base. SigProfilerMatrixGenerator uses as a standard the pyrimidine classification

File	# of sequences
test.SBS6.all	Pyrimidine single nucleotide variants, C > {A, G, or T} and T > {A, G, or C} = 6
test.SBS24.all	test.SBS6.all (6) x 4 transcriptional bias categories = 24
test.SBS96.all	Possible starting nucleotides (4) x test.SBS6.all (6) x possible ending nucleotides (4)= 96 total combinations
test.SBS384.all	test.SBS96.all (96) x 4 transcriptional bias categories = 384
test.SBS1536.all	Possible starting dinucleotides (16) x test.SBS6.all (6) x possible ending dinucleotides (16) = 1536 total combinations
test.SBS6124.all	test.SBS1536.all (1536) x 4 transcriptional bias categories = 6144

SBS-6

The test.SBS6.all file contains the frequency of each of the 6 pyrimidine single nucleotide variants, C > {A, G, or T} and T > {A, G, or C} detected in each input sample.

enter image description here The above image is a screenshot of the generated file. Here, on line 3, C>G corresponds to a C to G mutation and each column is the frequency of that mutation in a specific sample (corresponding column header).

SBS-24

The test.SBS24.all file separates each of the 6 pyrimidine single nucleotide variants, C > {A, G, or T} and T > {A, G, or C} detected into the 4 transcriptional strand bias categories. 6 x 4 = 24 total combinations

enter image description here The above image is a screenshot of the generated file. Here, on line 4, T:C>T corresponds to a C to T mutation on the transcribed strand.

SBS-96 ###

The test.SBS96.all file contains all of the following the pyrimidine single nucleotide variants, N[{C > A, G, or T} or {T > A, G, or C}]N.

4 possible starting nucleotides x 6 pyrimidine variants x 4 ending nucleotides = 96 total combinations.

enter image description here The above image is a screenshot of the generated file. Here, on line 6, A[C>G]A corresponds to a ACA mutating to AGA.

SBS-384

The test.SBS384.all file separates each nucleotide combination in the test.SBS96.all file into the 4 transcriptional strand bias categories.

96 sequences x 4 categories = 384 total combinations.

enter image description here The above image is a screenshot of the generated file. Here, on line 7, T:A[C>G]C corresponds to a ACC mutating to AGC on the transcribed strand.

SBS-1536

The test.SBS1536.all file contains all of the following the pyrimidine single nucleotide variants, NN[{C > A, G, or T} or {T > A, G, or C}]NN.

16 (4x4) possible starting dinucleotides x 6 pyrimidine variants x 16 (4x4) possible ending dinucleotides = 1536 total combinations.

enter image description here The above image is a screenshot of the generated file. Here, on line 8, AA[C>A]CG corresponds to a AACCG mutating to AAACG.

SBS-6144

The test.SBS6144.all file separates each nucleotide combination in the test.SB1536.all file into the 4 transcriptional strand bias categories.

1536 sequences x 4 categories = 6144 total combinations.

enter image description here The above image is a screenshot of the generated file. Here, on line 9, T:AA[C>A]CT corresponds to a AACCT mutating to AAACT on the transcribed strand.