The additional Tables A-D, and Figures A-D.

Table A in S1 File. The numbers of scaffolds selected, mutagens categorized as the selected scaffold and the ratios of C1 to S for different mutagenicity cutoffs. (C1: number of mutagenic compounds, S: number of mutagenic scaffolds); Table B in S1 File. The numbers of scaffolds selected, non-mutagens categorized as the selected scaffold and ratios of C2 to S for different mutagenicity cutoffs. (C2: number of non-mutagenic compounds, S: number of non-mutagenic scaffolds); Table C in S1 File. Rate of mutagen and number of compounds for each scaffold in: major mutagenic scaffold groups (Acridine, Phenanthrene, Pyrene, Quinoxaline), minor mutagenic scaffold group (Naphthalene), and scaffold groups which cannot be classified as either major or minor mutagenic groups (Benzene, Quinoline); Table D in S1 File. Overview of the selected scaffolds; Fig A in S1 File. The example of non-mutagenic compounds having the structural alert of “Polycyclic Aromatic Hydrocarbons”; Fig B in S1 File. The non-mutagenic compounds containing the non-mutagenic scaffolds of N-phenyl-quinoline-8-sulfonamide (39), and 1,3,5-triazine (40); Fig C in S1 File. The major scaffolds contributing to Ames mutagenicity; Fig D in S1 File. Scaffolds having mutagenic tendencies. (PDF)