Table 1.

Summary of the SBS detected at ≥ 3x per-base coverage and of the AA-signature analysis results

Case IDTotal SBSSBS per MbpA > T SBSA > T per MbpA>T (%)CAG context (%)SB A > T ratio (NTr/Tr)SBaP valueSB FDR Q valueContribution to Sig 22 (AA)AA signature
EN-01-RP6089.13765.661.826.13.3 (272/82)00380 (63%)Yes
EN-01-B2994.5560.818.712.52.1 (37/18)0.015153 (18%)Yesb
EN-02-RP98414.75858.759.526.73.1 (424/136)00514 (52%)Yes
EN-02-U88913.35297.959.526.13.3 (384/118)00457 (51%)Yes
EN-03-RP80712.04436.654.925.02.0 (278/140)2.1E–111.7E–09402 (50%)Yes
EN-04-RP6399.52413.637.719.52.3 (157/68)4.4E–093.6E–07164 (26%)Yes
EN-05-RP3495.21151.733.019.12.8 (79/28)1.3E–061.1E–0487 (25%)Yes
EN-06-RP3525.3150.24.30.05.5 (11/2)0.02710 (0%)
EN-07-B4406.6350.58.011.41.2 (15/13)0.85010 (0%)
EN-08-U155123.1119517.877.023.42.8 (840/303)001391 (90%)Yes
EN-09-U222133.1170125.476.627.42.7 (1185/431)001931 (87%)Yes
EN-10-U270740.4148622.254.926.22.8 (1052/377)002706 (100%)Yes
EN-11-U66910.03094.646.226.92.5 (211/85)3.7E-130297 (44%)Yes
Non-EN-01-RP3855.7240.46.20.00.6 (9/14)0.40010 (0%)
Non-EN-02-RP2583.9140.25.414.35.0 (10/2)0.04310 (0%)

NOTE: Suffixes -B, -RP, and -U indicate bladder, renal pelvis, and ureter, respectively.

Abbreviations: SBS, single base substitution; Mbp, megabase pair; A > T, A > T transversion(s); SB A > T, strand bias, the ratio of A > T transversions on the non-transcribed versus transcribed strand (the number of respective transversions is shown in brackets); CAG context (%), percentage of A > T transversions in the most frequent context reported for the AA signature; NTr/Tr, ratio of A>T variants on nontranscribed versus transcribed strand; SB P value and FDR q value, measures of significance of the strand bias, see Materials and Methods. Contribution to Sig 22 (AA) (Sig = NMF-determined mutational signature) shown as the number of SBS and the corresponding percentage (in brackets) of the total SBS per sample. AA signature, positivity for AA signature considering the co-occurrence of ≥ 50 SBS and ≥ 15% A > T, ≥ 20% CAG context, strand bias (SB) and its significance (SB P and/or q value) and mutation load contribution to Sig 22 (AA), as described previously (9).

  • aZero values correspond to a P value below 2 × 10−16.

  • bLower percentage in the 5′-CpApG-3′ context and nonsignificant q value; supported by the NMF analysis.