<h1> Single Base Substitution (SBS) </h1> @[toc](Quick Links) - [Using the Tool - **Output**][1] --- ## Overview ##  <br>  <br> 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.  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  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.  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.  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.  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.  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. [1]: https://osf.io/s93d5/wiki/4.%20Using%20the%20Tool%20-%20Output/