Column Title	Description
Sample	Unique tumor identifier from TCGA
A_T_coord_clusters	the number of clusters in a sample composed either entirely of base substitutions at adenines or entirely of base substitutions at thymines.
G_C_coord_clusters	the number of clusters in a sample composed either entirely of base substitutions at guanines or entirely of base substitutions at cytosines.
Non_coord_clusters	the number of clusters in a sample composed of any mix of mutation types.
clusters	the total number of clusters identified in a sample.
mutations	the total number of mutations identified in a sample.
complex	the total number of complex mutations (multiple sequence changes within 10 nucleotides of each other) identified in a sample.
insertions	the total number of insertions identified in a sample.
deletions	the total number of deletions identified in a sample.
indels	the total number of insertions and deletions identified in a sample.
substitutions	the total number of base substitutions identified in a sample.
bases	the total number of bases within all 41 nucleotide sequence contexts in a sample.  This is equivalent to the number of base substitutions in a sample multiplied by 41.
A_to_T	the total number of adenine to thymine substitutions in a sample.
A_to_G	the total number of adenine to guanine substitutions in a sample.
A_to_C	the total number of adenine to cytosine substitutions in a sample.
A	the total number of adenine substitutions in a sample.
a	the total number of adenines present within all the 41 nucleotide contexts analyzed in a sample.
T_to_A	the total number of thymine to adenine substitutions in a sample.
T_to_C	the total number of thymine to cytosine substitutions in a sample.
T_to_G	the total number of thymine to guanine substitutions in a sample.
T	the total number of thymine substitutions in a sample.
t	the total number of thymines present within all the 41 nucleotide contexts analyzed in a sample.
G_to_C	the total number of guanine to cytosine substitutions in a sample.
G_to_T	the total number of guanine to thymine substitutions in a sample.
G_to_A	the total number of guanine to adenine substitutions in a sample.
G	the total number of guanine substitutions in a sample.
g	the total number of guanines present within all the 41 nucleotide contexts analyzed in a sample.
C_to_G	the total number of cytosine to guanine substitutions in a sample.
C_to_A	the total number of cytosine to adenine substitutions in a sample.
C_to_T	the total number of cytosine to thymine substitutions in a sample.
C	the total number of cytosine substitutions in a sample.
c	the total number of cytosines present within all the 41 nucleotide contexts analyzed in a sample.
tCw_to_G	the total number of cytosine to guanine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by either a 3’ adenine or thymine (i.e. the number of times the sequence TCW is changed to TGW in a sample).
tCw_to_A	the total number of cytosine to adenine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by either a 3’ adenine or thymine (i.e. the number of times the sequence TCW is changed to TAW in a sample).
tCw_to_T	the total number of cytosine to thymine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by either a 3’ adenine or thymine (i.e. the number of times the sequence TCW is changed to TTW in a sample).
tCw	"the total number of cytosine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by either a 3’ adenine or thymine (i.e. the number of times the sequence TCW is changed to TDW in a sample, where D is A, G or T)."
tcw	the total number of times the sequence tct and tca occur in all of the 41 nucleotide sequence contexts of a sample.
tCw_per_mut	The fraction of total mutations in a sample that involve the substitution of a cytosine preceded by a 5’ thymine and followed by either a 3’ adenine or thymine.  This is calculated by dividing the value for “tCw” by the value for “mutations.”
tCw_per_C	The fraction of total substituted cytosines in a sample that occur with a 5’ thymine and either a 3’ adenine or thymine. This is calculated by dividing the value for “tCw” by the value for “C.”
tcw_per_c	The fraction of total cytosines in all the 41 nucleotide sequence contexts in a sample that occur with a 5’ thymine and either a 3’ adenine or thymine. This is calculated by dividing the value for “tcw” by the value for “c.”
enrich_tCw	The fold enrichment of cytosine substitutions preceded by a 5’ thymine and followed by a 3’ adenine or thymine among all cytosines over the fraction of cytosines in 41 nucleotide sequence contexts that occur in the contexts of tct and tca.  This is calculated by dividing the value for “tCw_per_C” by the value for “tcw_per_c.”
freq_tCw	the fraction of tct and tca sequences in all the 41 nucleotide contexts in a sample where the cytosine is substituted.  This is calculated by dividing the value for “tCw” by the value for “tcw.”
wGa_to_C	the total number of guanine to cytosine substitutions in a sample where the mutated guanine is preceded by either a 5’ adenine or thymine and followed by a 3’ adenine (i.e. the number of times the sequence WGA is changed to WCA in a sample).
wGa_to_T	the total number of guanine to thymine substitutions in a sample where the mutated guanine is preceded by either a 5’ adenine or thymine and followed by a 3’ adenine (i.e. the number of times the sequence WGA is changed to WTA in a sample).
wGa_to_A	the total number of guanine to adenine substitutions in a sample where the mutated guanine is preceded by either a 5’ adenine or thymine and followed by a 3’ adenine (i.e. the number of times the sequence WGA is changed to WAA in a sample).
wGa	"the total number of guanine substitutions in a sample where the mutated guanine is preceded by either a 5’ adenine or thymine and followed by a 3’ adenine (i.e. the number of times the sequence WGA is changed to WHA in a sample, where H is A, C or T)."
wga	the total number of times the sequence tga and aga occur in all of the 41 nucleotide sequence contexts of a sample.
wGa_per_mut	The fraction of total mutations in a sample that involve the substitution of a guanine preceded by either a 5’ adenine or thymine and followed by either a 3’ adenine.  This is calculated by dividing the value for “wGa” by the value for “mutations.”
wGa_per_G	The fraction of total substituted guanines in a sample that occur with either a 5’ adenine or thymine and a 3’ adenine. This is calculated by dividing the value for “wGa” by the value for “G.”
wga_per_g	The fraction of total guanines in all the 41 nucleotide sequence contexts in a sample that occur with either a 5’ adenine or thymine and a 3’ adenine. This is calculated by dividing the value for “wga” by the value for “g.”
enrich_wGa	The fold enrichment of guanine substitutions preceded by either a 5’ adenine or thymine and followed by a 3’ adenine among all guanines over the fraction of guanines in 41 nucleotide sequence contexts that occur in the contexts of tga and aga.  This is calculated by dividing the value for “wGa_per_G” by the value for “wga_per_g.”
freq_wGa	the fraction of tga and aga sequences in all the 41 nucleotide contexts in a sample where the guanine is substituted.  This is calculated by dividing the value for “wGa” by the value for “wga.”
[tCw_to_G+tCw_to_T]_per_mut	"The fraction of total mutations in a sample that are APOBEC signature mutations, i.e. the fraction of total mutations in a sample that fit one of the following:- cytosine to guanine substitutions in the sequences tct or tca, -cytosine to thymine substitutions in the sequences tct or tca, -guanine to cytosine substitutions in the sequences tga or aga, - guanine to adenine substitutions in the sequences tga or aga.  This is calculated by adding the values in the columns “tCw_to_G,” “tCw_to_T,” “wGa_to_C,” “wGa_to_A” and then dividing the resulting total by the value in “mutations.”"
tCw_to_G+tCw_to_T	"The total number of APOBEC signature mutations in a sample, i.e. the number of cytosine to guanine substitutions in the sequences tct or tca, cytosine to thymine substitutions in the sequences tct or tca, guanine to cytosine substitutions in the sequences tga or aga, and guanine to adenine substitutions in the sequences tga or aga in the specified sample."
[(C_to_G)+(C_to_T)]-[(tCw_to_G)+(tCw_to_T)]	"the number of cytosine to guanine, and cytosine to thymine substitutions that do not occur in the sequences tct and tca plus the number of guanine to cytosine and guanine to adenine substitutions that do not occur in a sequence context of tga or aga for a sample.  This is calculated by adding the values in columns “G_to_C,” “G_to_A,” “C_to_G,” and “C_to_T” and subtracting from the resulting total the value from “tCw_to_G+tCw_to_T.”"
tcw+wga	"the number of times the sequences tct, tca, tga, and aga occur in all the 41 nucleotide sequence contexts in a sample.  This is calculated by adding the values in “tcw” and “wga”"
c-tcw	"the number of cytosines and guanines in all the 41 nucleotide contexts in a sample that do not occur in the sequences tct, tca, or tga, aga respectively.  This is calculated by adding the values in “c” and “g” and subtracting from the total the value in “tcw+wga.”"
Fisher_p-value_tCw	"p-value for statistical over-representation of APOBEC signature mutations in a sample.  The p-value produced by comparing for each sample the ratio of “tCw_to_G+tCw_to_T” to “[(C_to_G)+(C_to_T)]-[(tCw_to_G)+(tCw_to_T)]” to the ratio of “tcw+wga” to “c-tcw” by a one sided Fisher’s exact text, predicting that the ratio of “tCw_to_G+tCw_to_T” to “[(C_to_G)+(C_to_T)]-[(tCw_to_G)+(tCw_to_T)]” is greater than the ratio of “tcw+wga” to “c-tcw”.  All samples for which this prediction is not true receive a p-value = 1"
BH_Fisher_p-value_tCw	Benjamini-Hochberg-corrected p-values for statistical over-representation of APOBEC signature mutations in a sample.  The resulting p-value generated by correcting the “Fisher_p-value_tCw” for multiple testing error by Benjamini-Hochberg (produced using p.adjust() in R).
bonferroni_Fisher_p-value_tCw	Bonferroni-corrected p-values for statistical over-representation of APOBEC signature mutations in a sample.  The resulting p-value generated by correcting the “Fisher_p-value_tCw” for multiple testing error by the Bonferroni method (produced using p.adjust() in R).
odds_ratio_tCw	the odds ratio calculated for the comparison of the ratio of “tCw_to_G+tCw_to_T” to “[(C_to_G)+(C_to_T)]-[(tCw_to_G)+(tCw_to_T)]” to the ratio of “tcw+wga” to “c-tcw” in each sample.
95%_confidence_lower_tCw	the lower boundary of the 95% confidence interval for the odds ratio calculated for each sample in “odds_ratio_tCw”.
95%_confidence_upper_tCw	"the upper boundary of the 95% confidence interval for the odds ratio calculated for each sample in “odds_ratio_tCw”.  Since this is a one sided Fisher’s test predicting that the ratio of “tCw_to_G+tCw_to_T” to “[(C_to_G)+(C_to_T)]-[(tCw_to_G)+(tCw_to_T)]” is greater than the ratio of “tcw+wga” to “c-tcw,” this value is reported as “Inf” for infinite."
APOBEC_enrich	"the enrichment over random of APOBEC pattern mutations.  This is calculated as: [(tCw_to_G+tCw_to_T)/ (C_to_G)+(C_to_T)]/[ tcw/c].  While not written in the formula, the complement sequences and mutations (i.e. wGa_to_A, wGa_to_C, G _to_A, G_to_C, wga, and g) are included in the value provided in the file."
tCw_to_G_enrich	"the enrichment over random of APOBEC signature mutations specifically involving C to G changes .  This is calculated as: [(tCw_to_G)/ (C_to_G)]/[ tcw/c].  While not written in the formula, the complement sequences and mutations (i.e. wGa_to_C, G_to_C, wga, and g) are included in the value provided in the file."
tCw_to_T_enrich	"the enrichment over random of APOBEC signature mutations specifically involving C to T changes .  This is calculated as: [(tCw_to_T)/ (C_to_T)]/[ tcw/c].  While not written in the formula, the complement sequences and mutations (i.e. wGa_to_A, G _to_A wga, and g) are included in the value provided in the file."
p-value_GvT_skew	"The p-value produced by comparing for each sample the ratio of [“tCw_to_G”+“wGa_to_C”] to “[“tCw” +""wGa""-“tCw_to_G”-“wGa_to_C”]” to the ratio of [“tCw_to_T”+“wGa_to_A”] to [“tCw” +""wGa""-“tCw_to_T”-“wGa_to_A”] by a two sided Fisher’s exact text"
BH_p-value_GvT_skew	The resulting p-value generated by correcting the “p-value_GvT_skew” for multiple testing error by Benjamini-Hochberg (produced using p.adjust() in R).
bonferroni_p-value_GvT_skew	The resulting p-value generated by correcting the “p-value_GvT_skew” for multiple testing error by the Bonferroni method (produced using p.adjust() in R).
non-APOBEC_mutations	"The total number of mutations in a sample that are not characterized by one of the following changes: TCA to TTA, TCA to TGA, TCT to TTT, TCT to TGT, AGA to AAA, AGA to ACA, TGA to TAA, or TGA to TCA.  This is calculated by substrating the value in ""tCw_to_G+tCw_to_T"" from the value in ""mutations"""
non-APOBEC_substitutions	"The total number of base substitutions in a sample that are not characterized by one of the following changes: TCA to TTA, TCA to TGA, TCT to TTT, TCT to TGT, AGA to AAA, AGA to ACA, TGA to TAA, or TGA to TCA.  This is calculated by substrating the value in ""tCw_to_G+tCw_to_T"" from the value in ""substitutions"""
APOBEC_MutLoad_MinEstimate	"A minimum estimate of the number of APOBEC induced mutations in a sample.  This estimate is calculated using the formula: [""tCw_to_G+tCw_to_T""]*[(""APOBEC_enrich""-1)/""APOBEC_enrich""] to determine the number of APOBEC signature mutations in excess of what would be expected by random mutagenesis.  Calculated values are rounded to the nearest whole number.  APOBEC_MutLoad_MinEstimate is calculated only for samples with a BH_Fisher_p-value_tCw value less than or equal to 0.05, signifying a statistical over-representaion of APOBEC mutagenesis.  Samples with BH_Fisher_p-value_tCw value greater than 0.05 receive a value of 0."
Cg_to_G	the total number of cytosine to guanine substitutions in a sample where the mutated cytosine is followed by a 3’ guanine (i.e. the number of times the sequence CG is changed to GG in a sample).
Cg_to_A	the total number of cytosine to adenine substitutions in a sample where the mutated cytosine is followed by a 3’ guanine (i.e. the number of times the sequence CG is changed to AG in a sample).
Cg_to_T	the total number of cytosine to thymine substitutions in a sample where the mutated cytosine is followed by a 3’ guanine (i.e. the number of times the sequence CG is changed to TG in a sample).
Cg	"the total number of cytosinesubstitutions in a sample where the mutated cytosine is followed by a 3’ guanine (i.e. the number of times the sequence CG is changed to DG in a sample, where D is A, G or T)."
cg	the total number of times the sequence cg occurs in all of the 41 nucleotide sequence contexts of a sample.
Cg_per_mut	The fraction of total mutations in a sample that involve the substitution of a cytosine followed by  a 3’ guanine.  This is calculated by dividing the value for “Cg” by the value for “mutations.”
Cg_per_C	The fraction of total substituted cytosines in a sample that occur with a 3’ guanine. This is calculated by dividing the value for “Cg” by the value for “C.”
cg_per_c	The fraction of total cytosines in all the 41 nucleotide sequence contexts in a sample that occur with a 3’ guanine This is calculated by dividing the value for “cg” by the value for “c.”
enrich_Cg	The fold enrichment of cytosine substitutions followed by a 3’ guanine among all substituted cytosines over the fraction of cytosines in 41 nucleotide sequence contexts that occur in the contexts of cg.  This is calculated by dividing the value for “Cg_per_C” by the value for “cg_per_c.”
freq_Cg	the fraction of cg sequences in all the 41 nucleotide contexts in a sample where the cytosine is substituted.  This is calculated by dividing the value for “Cg” by the value for “cg.”
cG_to_C	the total number of guanine to cytosine substitutions in a sample where the mutated guanine is preceded by a 5’ cytosine (i.e. the number of times the sequence CG is changed to CC in a sample).
cG_to_T	the total number of guanine to thymine substitutions in a sample where the mutated guanine is preceded by either a 5’ cytosine (i.e. the number of times the sequence CG is changed to CT in a sample).
cG_to_A	the total number of guanine to adenine substitutions in a sample where the mutated guanine is preceded by either a 5’ cytosine (i.e. the number of times the sequence CG is changed to CA in a sample).
cG	"the total number of guanine substitutions in a sample where the mutated guanine is preceded by either a 5’ cytosine (i.e. the number of times the sequence CG is changed to CH in a sample, where H is A, C or T)."
cg	the total number of times the sequence cg occurs in all of the 41 nucleotide sequence contexts of a sample.
cG_per_mut	The fraction of total mutations in a sample that involve the substitution of a guanine preceded by  a 5’ cytosine.  This is calculated by dividing the value for “cG” by the value for “mutations.”
cG_per_G	The fraction of total substituted guanines in a sample that occur with a 5’ cytosine. This is calculated by dividing the value for “cG” by the value for “G.”
cg_per_g	The fraction of total guanines in all the 41 nucleotide sequence contexts in a sample that occur with a 5’ cytosine. This is calculated by dividing the value for “cg” by the value for “g.”
enrich_cG	The fold enrichment of guanine substitutions preceded by a 5’ cytosine among all substituted guanines over the fraction of guanines in 41 nucleotide sequence contexts that occur in the contexts of cg.  This is calculated by dividing the value for “cG_per_G” by the value for “cg_per_g.”
freq_cG	the fraction of cg sequences in all the 41 nucleotide contexts in a sample where the guanine is substituted.  This is calculated by dividing the value for “cG” by the value for “cg.”
tCa_to_G	the total number of cytosine to guanine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by a 3’ adenine (i.e. the number of times the sequence TCA is changed to TGA in a sample).
tCa_to_A	the total number of cytosine to adenine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by a 3’ adenine (i.e. the number of times the sequence TCA is changed to TAA in a sample).
tCa_to_T	the total number of cytosine to thymine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by a 3’ adenine (i.e. the number of times the sequence TCA is changed to TTA in a sample).
tCa	"the total number of cytosine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by a 3’ adenine (i.e. the number of times the sequence TCA is changed to TDA in a sample, where D is A, G or T)."
tca	the total number of times the sequence tca occurs in all of the 41 nucleotide sequence contexts of a sample.
tCa_per_mut	The fraction of total mutations in a sample that involve the substitution of a cytosine preceded by a 5’ thymine and followed by a 3’ adenine.  This is calculated by dividing the value for “tCa” by the value for “mutations.”
tCa_per_C	The fraction of total substituted cytosines in a sample that occur with a 5’ thymine and a 3’ adenine. This is calculated by dividing the value for “tCa” by the value for “C.”
tca_per_c	The fraction of total cytosines in all the 41 nucleotide sequence contexts in a sample that occur with a 5’ thymine and a 3’ adenine. This is calculated by dividing the value for “tca” by the value for “c.”
enrich_tCa	The fold enrichment of cytosine substitutions preceded by a 5’ thymine and followed by a 3’ adenine among all substituted cytosines over the fraction of cytosines in 41 nucleotide sequence contexts that occur in the context of tca.  This is calculated by dividing the value for “tCa_per_C” by the value for “tca_per_c.”
freq_tCa	the fraction of tca sequences in all the 41 nucleotide contexts in a sample where the cytosine is substituted.  This is calculated by dividing the value for “tCa” by the value for “tca.”
tGa_to_C	the total number of guanine to cytosine substitutions in a sample where the mutated guanine is preceded by a 5’thymine and followed by a 3’ adenine (i.e. the number of times the sequence TGA is changed to TCA in a sample).
tGa_to_T	the total number of guanine to thymine substitutions in a sample where the mutated guanine is preceded by a 5’ thymine and followed by a 3’ adenine (i.e. the number of times the sequence TGA is changed to TTA in a sample).
tGa_to_A	the total number of guanine to adenine substitutions in a sample where the mutated guanine is preceded by a 5’ thymine and followed by a 3’ adenine (i.e. the number of times the sequence TGA is changed to TAA in a sample).
tGa	"the total number of guanine substitutions in a sample where the mutated guanine is preceded by a 5’ thymine and followed by a 3’ adenine (i.e. the number of times the sequence TGA is changed to THA in a sample, where H is A, C or T)."
tga	the total number of times the sequence tga occurs in all of the 41 nucleotide sequence contexts of a sample.
tGa_per_mut	The fraction of total mutations in a sample that involve the substitution of a guanine preceded by a 5’ thymine and followed by a 3’ adenine.  This is calculated by dividing the value for “tGa” by the value for “mutations.”
tGa_per_G	The fraction of total substituted guanines in a sample that occur with a 5’ thymine and a 3’ adenine. This is calculated by dividing the value for “tGa” by the value for “G.”
tga_per_g	The fraction of total guanines in all the 41 nucleotide sequence contexts in a sample that occur with a 5’ thymine and a 3’ adenine. This is calculated by dividing the value for “tga” by the value for “g.”
enrich_tGa	The fold enrichment of guanine substitutions preceded by  a 5’ thymine and followed by a 3’ adenine among all substituted guanines over the fraction of guanines in 41 nucleotide sequence contexts that occur in the context of tga.  This is calculated by dividing the value for “tGa_per_G” by the value for “tga_per_g.”
freq_tGa	the fraction of tga sequences in all the 41 nucleotide contexts in a sample where the guanine is substituted.  This is calculated by dividing the value for “tGa” by the value for “tga.”
tCt_to_G	the total number of cytosine to guanine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by a 3’ thymine (i.e. the number of times the sequence TCT is changed to TGT in a sample).
tCt_to_A	the total number of cytosine to adenine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by a 3’ thymine (i.e. the number of times the sequence TCT is changed to TAT in a sample).
tCt_to_T	the total number of cytosine to thymine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by a 3’ thymine (i.e. the number of times the sequence TCT is changed to TTT in a sample).
tCt	"the total number of cytosine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by a 3’ thymine (i.e. the number of times the sequence TCT is changed to TDT in a sample, where D is A, G or T)."
tct	the total number of times the sequence tct occurs in all of the 41 nucleotide sequence contexts of a sample.
tCt_per_mut	The fraction of total mutations in a sample that involve the substitution of a cytosine preceded by a 5’ thymine and followed by a 3’ thymine.  This is calculated by dividing the value for “tCt” by the value for “mutations.”
tCt_per_C	The fraction of total substituted cytosines in a sample that occur with a 5’ thymine and a 3’ thymine. This is calculated by dividing the value for “tCt” by the value for “C.”
tct_per_c	The fraction of total cytosines in all the 41 nucleotide sequence contexts in a sample that occur with a 5’ thymine and a 3’ thymine. This is calculated by dividing the value for “tct” by the value for “c.”
enrich_tCt	The fold enrichment of cytosine substitutions preceded by a 5’ thymine and followed by a 3’ thymine among all substituted cytosines over the fraction of cytosines in 41 nucleotide sequence contexts that occur in the context of tct.  This is calculated by dividing the value for “tCt_per_C” by the value for “tct_per_c.”
freq_tCt	the fraction of tct sequences in all the 41 nucleotide contexts in a sample where the cytosine is substituted.  This is calculated by dividing the value for “tCt” by the value for “tct.”
aGa_to_C	the total number of guanine to cytosine substitutions in a sample where the mutated guanine is preceded by a 5’ adenine and followed by a 3’ adenine (i.e. the number of times the sequence AGA is changed to ACA in a sample).
aGa_to_T	the total number of guanine to thymine substitutions in a sample where the mutated guanine is preceded by a 5’ adenine and followed by a 3’ adenine (i.e. the number of times the sequence AGA is changed to ATA in a sample).
aGa_to_A	the total number of guanine to adenine substitutions in a sample where the mutated guanine is preceded by a 5’ adenine and followed by a 3’ adenine (i.e. the number of times the sequence AGA is changed to AAA in a sample).
aGa	"the total number of guanine substitutions in a sample where the mutated guanine is preceded by a 5’ adenine and followed by a 3’ adenine (i.e. the number of times the sequence AGA is changed to AHA in a sample, where H is A, C or T)."
aga	the total number of times the sequence aga occurs in all of the 41 nucleotide sequence contexts of a sample.
aGa_per_mut	The fraction of total mutations in a sample that involve the substitution of a guanine preceded by a 5’ adenineand followed by  a 3’ adenine.  This is calculated by dividing the value for “aGa” by the value for “mutations.”
aGa_per_G	The fraction of total substituted guanines in a sample that occur with a 5’ adenine and a 3’ adenine. This is calculated by dividing the value for “aGa” by the value for “G.”
aga_per_g	The fraction of total guanines in all the 41 nucleotide sequence contexts in a sample that occur with a 5’ adenine and a 3’ adenine. This is calculated by dividing the value for “aga” by the value for “g.”
enrich_aGa	The fold enrichment of guanine substitutions preceded by a 5’ adenine and followed by a 3’ adenine among all substituted guanines over the fraction of guanines in 41 nucleotide sequence contexts that occur in the context of aga.  This is calculated by dividing the value for “aGa_per_G” by the value for “aga_per_g.”
freq_aGa	the fraction of aga sequences in all the 41 nucleotide contexts in a sample where the guanine is substituted.  This is calculated by dividing the value for “aGa” by the value for “aga.”
tC_to_G	the total number of cytosine to guanine substitutions in a sample where the mutated cytosine is preceeded by a 5' thymine (i.e. the number of times the sequence TC is changed to TG in a sample).
tC_to_A	the total number of cytosine to adenine substitutions in a sample where the mutated cytosine is preceeded by a 5' thymine (i.e. the number of times the sequence TC is changed to TA in a sample).
tC_to_T	the total number of cytosine to thymine substitutions in a sample where the mutated cytosine is preceeded by a 5' thymine (i.e. the number of times the sequence TC is changed to TT in a sample).
tC	"the total number of cytosine substitutions in a sample where the mutated cytosine is preceeded by a 5' thymine (i.e. the number of times the sequence TC is changed to TD in a sample, where D is A, G or T)."
tc	the total number of times the sequence tc occurs in all of the 41 nucleotide sequence contexts of a sample.
tC_per_mut	The fraction of total mutations in a sample that involve the substitution of a cytosine preceeded by a 5' thymine.  This is calculated by dividing the value for “tC” by the value for “mutations.”
tC_per_C	The fraction of total substituted cytosines in a sample that occur with a 5’ thymine.  This is calculated by dividing the value for “tC” by the value for “C.”
tc_per_c	The fraction of total cytosines in all the 41 nucleotide sequence contexts in a sample that occur with a 5’ thymine.  This is calculated by dividing the value for “tc” by the value for “c.”
enrich_tC	The fold enrichment of cytosine substitutions preceeded by a 5' thymine among all substituted cytosines over the fraction of cytosines in 41 nucleotide sequence contexts that occur in the contexs of tc.  This is calculated by dividing the value for “tC_per_C” by the value for “tc_per_c.”
freq_tC	the fraction of tc sequences in all the 41 nucleotide contexts in a sample where the cytosine is substituted.  This is calculated by dividing the value for “tC” by the value for “tc.”
Ga_to_C	the total number of guanine to cytosine substitutions in a sample where the mutated guanine is followed by a 3’ adenine (i.e. the number of times the sequence GA is changed to CA in a sample).
Ga_to_T	the total number of guanine to thymine substitutions in a sample where the mutated guanine is followed by a 3’ adenine (i.e. the number of times the sequence GA is changed to TA in a sample).
Ga_to_A	the total number of guanine to adenine substitutions in a sample where the mutated guanine is followed by a 3’ adenine (i.e. the number of times the sequence GA is changed to AA in a sample).
Ga	"the total number of guanine substitutions in a sample where the mutated guanine is followed by a 3’ adenine (i.e. the number of times the sequence GA is changed to HA in a sample, where H is A, C or T)."
ga	the total number of times the sequence ga occurs in all of the 41 nucleotide sequence contexts of a sample.
Ga_per_mut	The fraction of total mutations in a sample that involve the substitution of a guanine followed by a 3’ adenine.  This is calculated by dividing the value for “Ga” by the value for “mutations.”
Ga_per_G	The fraction of total substituted guanines in a sample that occur with a 3’ adenine. This is calculated by dividing the value for “Ga” by the value for “G.”
ga_per_g	The fraction of total guanines in all the 41 nucleotide sequence contexts in a sample that occur with a 3’ adenine. This is calculated by dividing the value for “ga” by the value for “g.”
enrich_Ga	The fold enrichment of guanine substitutions followed by a 3’ adenine among all substituted guanines over the fraction of guanines in 41 nucleotide sequence contexts that occur in the context of ga.  This is calculated by dividing the value for “Ga_per_G” by the value for “ga_per_g.”
freq_Ga	the fraction of ga sequences in all the 41 nucleotide contexts in a sample where the guanine is substituted.  This is calculated by dividing the value for “Ga” by the value for “ga.”
tCh_to_G	"the total number of cytosine to guanine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by either a 3’ adenine, cytosine or thymine (i.e. the number of times the sequence TCH is changed to TGH in a sample)."
tCh_to_A	"the total number of cytosine to adenine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by either a 3’ adenine, cytosine or thymine (i.e. the number of times the sequence TCH is changed to TAH in a sample)."
tCh_to_T	"the total number of cytosine to thymine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by either a 3’ adenine, cytosine or thymine (i.e. the number of times the sequence TCH is changed to TTH in a sample)."
tCh	"the total number of cytosine substitutions in a sample where the mutated cytosine is preceded by a 5’ thymine and followed by either a 3’ adenine, cytosine or thymine (i.e. the number of times the sequence TCH is changed to TDH in a sample, where D is A, G or T)."
tch	"the total number of times the sequence tct, tcc and tca occur in all of the 41 nucleotide sequence contexts of a sample."
tCh_per_mut	"The fraction of total mutations in a sample that involve the substitution of a cytosine preceded by a 5’ thymine and followed by either a 3’ adenine, cytosine or thymine.  This is calculated by dividing the value for “tCh” by the value for “mutations.”"
tCh_per_C	"The fraction of total substituted cytosines in a sample that occur with a 5’ thymine and either a 3’ adenine, cytosine or thymine. This is calculated by dividing the value for “tCh” by the value for “C.”"
tch_per_c	"The fraction of total cytosines in all the 41 nucleotide sequence contexts in a sample that occur with a 5’ thymine and either a 3’ adenine, cytosine or thymine. This is calculated by dividing the value for “tch” by the value for “c.”"
enrich_tCh	"The fold enrichment of cytosine substitutions preceded by a 5’ thymine and followed by a 3’ adenine, cytosine or thymine among all substituted cytosines over the fraction of cytosines in 41 nucleotide sequence contexts that occur in the contexts of tct, tcc and tca.  This is calculated by dividing the value for “tCh_per_C” by the value for “tch_per_c.”"
freq_tCh	"the fraction of tct, tcc and tca sequences in all the 41 nucleotide contexts in a sample where the cytosine is substituted.  This is calculated by dividing the value for “tCh” by the value for “tch.”"
dGa_to_C	"the total number of guanine to cytosine substitutions in a sample where the mutated guanine is preceded by either a 5’ adenine, guanine or thymine and followed by a 3’ adenine (i.e. the number of times the sequence DGA is changed to DCA in a sample)."
dGa_to_T	"the total number of guanine to thymine substitutions in a sample where the mutated guanine is preceded by either a 5’ adenine, guanine or thymine and followed by a 3’ adenine (i.e. the number of times the sequence DGA is changed to DTA in a sample)."
dGa_to_A	"the total number of guanine to adenine substitutions in a sample where the mutated guanine is preceded by either a 5’ adenine, guanine or thymine and followed by a 3’ adenine (i.e. the number of times the sequence DGA is changed to DAA in a sample)."
dGa	"the total number of guanine substitutions in a sample where the mutated guanine is preceded by either a 5’ adenine, guanine or thymine and followed by a 3’ adenine (i.e. the number of times the sequence DGA is changed to DHA in a sample, where H is A, C or T)."
dga	"the total number of times the sequence tga, gga and aga occur in all of the 41 nucleotide sequence contexts of a sample."
dGa_per_mut	"The fraction of total mutations in a sample that involve the substitution of a guanine preceded by either a 5’ adenine, guanine or thymine and followed by either a 3’ adenine.  This is calculated by dividing the value for “dGa” by the value for “mutations.”"
dGa_per_G	"The fraction of total substituted guanines in a sample that occur with either a 5’ adenine, guanine or thymine and a 3’ adenine. This is calculated by dividing the value for “dGa” by the value for “G.”"
dga_per_g	"The fraction of total guanines in all the 41 nucleotide sequence contexts in a sample that occur with either a 5’ adenine, guanine or thymine and a 3’ adenine. This is calculated by dividing the value for “dga” by the value for “g.”"
enrich_dGa	"The fold enrichment of guanine substitutions preceded by either a 5’ adenine, guanine or thymine and followed by a 3’ adenine among all substituted guanines over the fraction of guanines in 41 nucleotide sequence contexts that occur in the contexts of tga, gga and aga.  This is calculated by dividing the value for “dGa_per_G” by the value for “dga_per_g.”"
freq_dGa	"the fraction of tga, gga and aga sequences in all the 41 nucleotide contexts in a sample where the guanine is substituted.  This is calculated by dividing the value for “dGa” by the value for “dga.”"
cC_to_G	the total number of cytosine to guanine substitutions in a sample where the mutated cytosine is preceeded by a 5' cytosine (i.e. the number of times the sequence CC is changed to CG in a sample).
cC_to_A	the total number of cytosine to adenine substitutions in a sample where the mutated cytosine is preceeded by a 5' cytosine (i.e. the number of times the sequence CC is changed to CA in a sample).
cC_to_T	the total number of cytosine to thymine substitutions in a sample where the mutated cytosine is preceeded by a 5' cytosine (i.e. the number of times the sequence CC is changed to CT in a sample).
cC	"the total number of cytosine substitutions in a sample where the mutated cytosine is preceeded by a 5' cytosine (i.e. the number of times the sequence CC is changed to CD in a sample, where D is A, G or T)."
cc	the total number of times the sequence cc occurs in all of the 41 nucleotide sequence contexts of a sample.
cC_per_mut	The fraction of total mutations in a sample that involve the substitution of a cytosine preceeded by a 5' cytosine.  This is calculated by dividing the value for “cC” by the value for “mutations.”
cC_per_C	The fraction of total substituted cytosines in a sample that occur with a 5’ cytosine.  This is calculated by dividing the value for “cC” by the value for “C.”
cc_per_c	The fraction of total cytosines in all the 41 nucleotide sequence contexts in a sample that occur with a 5’ cytosine.  This is calculated by dividing the value for “cc” by the value for “c.”
enrich_cC	The fold enrichment of cytosine substitutions preceeded by a 5' cytosine among all substituted cytosines over the fraction of cytosines in 41 nucleotide sequence contexts that occur in the contexs of cc.  This is calculated by dividing the value for “cC_per_C” by the value for “cc_per_c.”
freq_cC	the fraction of cc sequences in all the 41 nucleotide contexts in a sample where the 3' cytosine is substituted.  This is calculated by dividing the value for “cC” by the value for “cc.”
Gg_to_C	the total number of guanine to cytosine substitutions in a sample where the mutated guanine is followed by a 3’ guanine (i.e. the number of times the sequence GG is changed to CG in a sample).
Gg_to_T	the total number of guanine to thymine substitutions in a sample where the mutated guanine is followed by a 3’ guanine (i.e. the number of times the sequence GG is changed to TG in a sample).
Gg_to_A	the total number of guanine to adenine substitutions in a sample where the mutated guanine is followed by a 3’ guanine (i.e. the number of times the sequence GG is changed to AG in a sample).
Gg	"the total number of guanine substitutions in a sample where the mutated guanine is followed by a 3’ guanine (i.e. the number of times the sequence GG is changed to HG in a sample, where H is A, C or T)."
gg	the total number of times the sequence gg occurs in all of the 41 nucleotide sequence contexts of a sample.
Gg_per_mut	The fraction of total mutations in a sample that involve the substitution of a guanine followed by a 3’ guanine.  This is calculated by dividing the value for “Gg” by the value for “mutations.”
Gg_per_G	The fraction of total substituted guanines in a sample that occur with a 3’ guanine. This is calculated by dividing the value for “Gg” by the value for “G.”
gg_per_g	The fraction of total guanines in all the 41 nucleotide sequence contexts in a sample that occur with a 3’ guanine. This is calculated by dividing the value for “gg” by the value for “g.”
enrich_Gg	The fold enrichment of guanine substitutions followed by a 3’ guanine among all substituted guanines over the fraction of guanines in 41 nucleotide sequence contexts that occur in the context of gg.  This is calculated by dividing the value for “Gg_per_G” by the value for “gg_per_g.”
freq_Gg	the fraction of gg sequences in all the 41 nucleotide contexts in a sample where the 5' guanine is substituted.  This is calculated by dividing the value for “Gg” by the value for “gg.”
wrC_to_G	the total number of cytosine to guanine substitutions in a sample where the two nucleotides preceeding the mutated cytosine on the 5’ side are either a thymine or adenine followed by either a guanine or adenine  (i.e. the number of times the sequence WRC is changed to WRG in a sample).
wrC_to_A	the total number of cytosine to adenine substitutions in a sample where the two nucleotides preceeding the mutated cytosine on the 5’ side are either a thymine or adenine followed by either a guanine or adenine  (i.e. the number of times the sequence WRC is changed to WRA in a sample).
wrC_to_T	the total number of cytosine to thymine substitutions in a sample where the two nucleotides preceeding the mutated cytosine on the 5’ side are either a thymine or adenine followed by either a guanine or adenine  (i.e. the number of times the sequence WRC is changed to WRA in a sample).
wrC	"the total number of cytosine substitutions in a sample where the two nucleotides preceeding the mutated cytosine on the 5’ side are either a thymine or adenine followed by either a guanine or adenine  (i.e. the number of times the sequence WRC is changed to WRD in a sample, where D is A, G or T)."
wrc	"the total number of times the sequences aac, tac, agc and tgc occur in all of the 41 nucleotide sequence contexts of a sample."
wrC_per_mut	The fraction of total mutations in a sample that involve the substitution of a cytosine were the preceeding two nucleotides on the 5' side are either a thymine or adenine followed by either a guanine or adenine.  This is calculated by dividing the value for “wrC” by the value for “mutations.”
wrC_per_C	The fraction of total substituted cytosines in a sample that occur with the two preceeding nucleotides on the 5’ side being either a thymine or guanine followed by either a guanine or adenine. This is calculated by dividing the value for “wrC” by the value for “C.”
wrc_per_c	The fraction of total cytosines in all the 41 nucleotide sequence contexts in a sample that occur with the two preceeding nucleotides on the 5’ side being either a thymine or adenine followed by  either a guanine or adenine. This is calculated by dividing the value for “wrc” by the value for “c.”
enrich_wrC	"The fold enrichment of cytosine substitutions with the two preceeding nucleotides on the 5’side being either a thymine or adenine  followed by a guanine or adenine among all substituted cytosines over the fraction of cytosines in 41 nucleotide sequence contexts that occur in the contexts of aac, tac, agc and tgc.  This is calculated by dividing the value for “wrC_per_C” by the value for “wrc_per_c.”"
freq_wrC	"the fraction of aac, tac, agc and tgc sequences in all the 41 nucleotide contexts in a sample where the cytosine is substituted.  This is calculated by dividing the value for “wrC” by the value for “wrc.”"
Gyw_to_C	the total number of guanine to cytosine substitutions in a sample where the two nucleotides following the mutated guanine on the 3’ side are either a cytosine or thymine followed by either a thymine or adenine  (i.e. the number of times the sequence GYW is changed to CYW in a sample).
Gyw_to_T	the total number of guanine to thymine substitutions in a sample where the two nucleotides following the mutated guanine on the 3’ side are either a cytosine or thymine followed by either a thymine or adenine  (i.e. the number of times the sequence GYW is changed to TYW in a sample).
Gyw_to_A	the total number of guanine to adenine substitutions in a sample where the two nucleotides following the mutated guanine on the 3’ side are either a cytosine or thymine followed by either a thymine or adenine  (i.e. the number of times the sequence GYW is changed to AYW in a sample).
Gyw	"the total number of guanine substitutions in a sample where the two nucleotides following the mutated guanine on the 3’ side are either a cytosine or thymine followed by either a thymine or adenine  (i.e. the number of times the sequence GYW is changed to HYW in a sample, where H is A, C or T)."
gyw	"the total number of times the sequences gca, gct, gta and gtt occur in all of the 41 nucleotide sequence contexts of a sample."
Gyw_per_mut	The fraction of total mutations in a sample that involve the substitution of a guanine were the following two nucleotides on the 3’ side are either a cytosine or thymine followed by either a thymine or adenine.  This is calculated by dividing the value for “Gyw” by the value for “mutations.”
Gyw_per_G	The fraction of total substituted guanines in a sample that occur with the two following nucleotides on the 3’ side are either a cytosine or thymine followed by either a thymine or adenine. This is calculated by dividing the value for “Gyw” by the value for “G.”
gyw_per_g	The fraction of total guanines in all the 41 nucleotide sequence contexts in a sample that occur with the two following nucleotides on the 3’ side are either a cytosine or thymine followed by either a thymine or adenine. This is calculated by dividing the value for “gyw” by the value for “g.”
enrich_Gyw	"The fold enrichment of guanine substitutions with the two following nucleotides on the 3’ side being either a cytosine or thymine followed by either a thymine or adenine among all substituted guanines over the fraction of guanines in 41 nucleotide sequence contexts that occur in the contexts of gca, gct, gta and gtt.  This is calculated by dividing the value for “Gyw_per_G” by the value for “gyw_per_g.”"
freq_Gyw	"the fraction of gca, gct, gta and gtt sequences in all the 41 nucleotide contexts in a sample where the guanine is substituted.  This is calculated by dividing the value for “Gyw” by the value for “gyw.”"
Cc_to_G	the total number of cytosine to guanine substitutions in a sample where the mutated cytosine is followed by a 3’ cytosine (i.e. the number of times the sequence CC is changed to GC in a sample).
Cc_to_A	the total number of cytosine to adenine substitutions in a sample where the mutated cytosine is followed by a 3’ cytosine (i.e. the number of times the sequence CC is changed to AC in a sample).
Cc_to_T	the total number of cytosine to thymine substitutions in a sample where the mutated cytosine is followed by a 3’ cytosine (i.e. the number of times the sequence CC is changed to TC in a sample).
Cc	"the total number of cytosine substitutions in a sample where the mutated cytosine is followed by a 3’ cytosine (i.e. the number of times the sequence CC is changed to DC in a sample, where D is A, G or T)."
cc	the total number of times the sequence cc occurs in all of the 41 nucleotide sequence contexts of a sample.
Cc_per_mut	The fraction of total mutations in a sample that involve the substitution of a cytosine followed by  a 3’ cytosine.  This is calculated by dividing the value for “Cc” by the value for “mutations.”
Cc_per_C	The fraction of total substituted cytosines in a sample that occur with a 3’ cytosine. This is calculated by dividing the value for “Cc” by the value for “C.”
cc_per_c	The fraction of total cytosines in all the 41 nucleotide sequence contexts in a sample that occur with a 3’ cytosine This is calculated by dividing the value for “cc” by the value for “c.”
enrich_Cc	The fold enrichment of cytosine substitutions followed by a 3’ cytosine among all substituted cytosines over the fraction of cytosines in 41 nucleotide sequence contexts that occur in the contexts of cc.  This is calculated by dividing the value for “Cc_per_C” by the value for “cc_per_c.”
freq_Cc	the fraction of cc sequences in all the 41 nucleotide contexts in a sample where the 5' cytosine is substituted.  This is calculated by dividing the value for “Cc” by the value for “cc.”
gG_to_C	the total number of guanine to cytosine substitutions in a sample where the mutated guanine is preceded by a 5’ guanine (i.e. the number of times the sequence GG is changed to GC in a sample).
gG_to_T	the total number of guanine to thymine substitutions in a sample where the mutated guanine is preceded by either a 5’ guanine (i.e. the number of times the sequence GG is changed to GT in a sample).
gG_to_A	the total number of guanine to adenine substitutions in a sample where the mutated guanine is preceded by either a 5’ guanine (i.e. the number of times the sequence GG is changed to GA in a sample).
gG	"the total number of guanine substitutions in a sample where the mutated guanine is preceded by either a 5’ guanine (i.e. the number of times the sequence GG is changed to GH in a sample, where H is A, C or T)."
gg	the total number of times the sequence gg occurs in all of the 41 nucleotide sequence contexts of a sample.
gG_per_mut	The fraction of total mutations in a sample that involve the substitution of a guanine preceded by  a 5’ guanine.  This is calculated by dividing the value for “gG” by the value for “mutations.”
gG_per_G	The fraction of total substituted guanines in a sample that occur with a 5’ guanine. This is calculated by dividing the value for “gG” by the value for “G.”
gg_per_g	The fraction of total guanines in all the 41 nucleotide sequence contexts in a sample that occur with a 5’ guanine. This is calculated by dividing the value for “gg” by the value for “g.”
enrich_gG	The fold enrichment of guanine substitutions preceded by a 5’ guanine among all substituted guanines over the fraction of guanines in 41 nucleotide sequence contexts that occur in the contexts of gg.  This is calculated by dividing the value for “gG_per_G” by the value for “gg_per_g.”
freq_gG	the fraction of gg sequences in all the 41 nucleotide contexts in a sample where the 3' guanine is substituted.  This is calculated by dividing the value for “gG” by the value for “gg.”
wA_to_T	the total number of adenine to thymine substitutions in a sample where the mutated adenine is preceded by either a 5’ adenine or thymine (i.e. the number of times the sequence WA is changed to WT in a sample).
wA_to_G	the total number of adenine to guanine substitutions in a sample where the mutated adenine is preceded by either a 5’ adenine or thymine (i.e. the number of times the sequence WA is changed to WG in a sample).
wA_to_C	the total number of adenine to cytosine substitutions in a sample where the mutated adenine is preceded by either a 5’ adenine or thymine (i.e. the number of times the sequence WA is changed to WC in a sample).
wA	"the total number of adenine substitutions in a sample where the mutated adenine is preceded by either a 5’ adenine or thymine (i.e. the number of times the sequence WA is changed to WB in a sample, where B is C, G or T)."
wa	the total number of times the sequence wa occurs in all of the 41 nucleotide sequence contexts of a sample.
wA_per_mut	The fraction of total mutations in a sample that involve the substitution of an adenine preceded by either a 5’ adenine or thymine.  This is calculated by dividing the value for “wA” by the value for “mutations.”
wA_per_A	The fraction of total substituted adenines in a sample that occur with either a 5’ adenine or thymine. This is calculated by dividing the value for “wA” by the value for “A.”
wa_per_a	The fraction of total adenines in all the 41 nucleotide sequence contexts in a sample that occur with either a 5’ adenine or thymine. This is calculated by dividing the value for “wa” by the value for “a.”
enrich_wA	The fold enrichment of adenine substitutions preceded by either a 5’ adenine or thymine among all substituted adenines over the fraction of guanines in 41 nucleotide sequence contexts that occur in the contexts of ta and aa.  This is calculated by dividing the value for “wA_per_A” by the value for “wa_per_a.”
freq_wA	the fraction of ta and aa sequences in all the 41 nucleotide contexts in a sample where the 3' adenine is substituted.  This is calculated by dividing the value for “wA” by the value for “wa.”
Tw_to_A	the total number of thymine to adenine substitutions in a sample where the mutated thymine is  followed by a 3’ adenine or thymine (i.e. the number of times the sequence TW is changed to AW in a sample).
Tw_to_C	the total number of thymine to cytosine substitutions in a sample where the mutated thymine is  followed by a 3’ adenine or thymine (i.e. the number of times the sequence TW is changed to CW in a sample).
Tw_to_G	the total number of thymine to guanine substitutions in a sample where the mutated thymine is  followed by a 3’ adenine or thymine (i.e. the number of times the sequence TW is changed to GW in a sample).
Tw	"the total number of thymine substitutions in a sample where the mutated thymine isfollowed by a 3’ adenine or thymine (i.e. the number of times the sequence TW is changed to VW in a sample, where V is A, C or G)."
tw	the total number of times the sequence tw occurs in all of the 41 nucleotide sequence contexts of a sample.
Tw_per_mut	The fraction of total mutations in a sample that involve the substitution of a thymine followed by either a 3’ adenine or thymine.  This is calculated by dividing the value for “Tw” by the value for “mutations.”
Tw_per_T	The fraction of total substituted thymines in a sample that occur with a 3’ adenine or thymine. This is calculated by dividing the value for “Tw” by the value for “T.”
tw_per_t	The fraction of total thymines in all the 41 nucleotide sequence contexts in a sample that occur with a 3’ adenine or thymine. This is calculated by dividing the value for “tw” by the value for “t.”
enrich_Tw	The fold enrichment of thymine substitutions followed by a 3’ adenine or thymine among all thymines over the fraction of thymines in 41 nucleotide sequence contexts that occur in the contexts of ta and tt.  This is calculated by dividing the value for “Tw_per_T” by the value for “tw_per_t.”
freq_Tw	the fraction of ta and tt sequences in all the 41 nucleotide contexts in a sample where the 5' thymine is substituted.  This is calculated by dividing the value for “Tw” by the value for “tw.”
reliable>=30	Indicates whether a calculation is based on the count of at least 30 mutations and therefore produces a reliable value. Placed to the right of any series of columns containing calculations for the respective count values of a specified motif.
Fisher_p-value_tCw_to_G	"The p-value produced by comparing for each sample the ratio of (“tCw_to_G"" + ""wGa_to_C”) to (""C_to_G"" + ""G_to_C"" - “tCw_to_G"" - ""wGa_to_C”) to the ratio of “tcw+wga” to “c-tcw” by a one sided Fisher’s exact text, predicting that the ratio of (“tCw_to_G"" + ""wGa_to_C”) to (""C_to_G"" + ""G_to_C"" - “tCw_to_G"" - ""wGa_to_C”) is greater than the ratio of “tcw+wga” to “c-tcw”.  All samples for which this prediction is not true receive a p-value = 1"
BH_Fisher_p-value_tCw_to_G	The resulting p-value generated by correcting the “Fisher_p-value_tCw_to_G” for multiple testing error by Benjamini-Hochberg (produced using p.adjust() in R).
bonferroni_Fisher_p-value_tCw_to_G	The resulting p-value generated by correcting the “Fisher_p-value_tCw_to_G” for multiple testing error by the Bonferroni method (produced using p.adjust() in R).
odds_ratio_tCw_to_G	"the odds ratio calculated for the comparison of the ratio of (“tCw_to_G"" + ""wGa_to_C”) to (""C_to_G"" + ""G_to_C"" - “tCw_to_G"" - ""wGa_to_C”) to the ratio of “tcw+wga” to “c-tcw” in each sample."
Fisher_p-value_tCw_to_T	"The p-value produced by comparing for each sample the ratio of (“tCw_to_T"" + ""wGa_to_A”) to (""C_to_T"" + ""G_to_A"" - “tCw_to_T"" - ""wGa_to_A”) to the ratio of “tcw+wga” to “c-tcw” by a one sided Fisher’s exact text, predicting that the ratio of (“tCw_to_T"" + ""wGa_to_A”) to (""C_to_T"" + ""G_to_A"" - “tCw_to_T"" - ""wGa_to_A”) is greater than the ratio of “tcw+wga” to “c-tcw”.  All samples for which this prediction is not true receive a p-value = 1"
BH_Fisher_p-value_tCw_to_T	The resulting p-value generated by correcting the “Fisher_p-value_tCw_to_T” for multiple testing error by Benjamini-Hochberg (produced using p.adjust() in R).
bonferroni_Fisher_p-value_tCw_to_T	The resulting p-value generated by correcting the “Fisher_p-value_tCw_to_T” for multiple testing error by the Bonferroni method (produced using p.adjust() in R).
odds_ratio_tCw_to_T	"the odds ratio calculated for the comparison of the ratio of (“tCw_to_T"" + ""wGa_to_A”) to (""C_to_T"" + ""G_to_A"" - “tCw_to_T"" - ""wGa_to_A”) to the ratio of “tcw+wga” to “c-tcw” in each sample."
