Additional file 1: of Characterizing Benzo[a]pyrene-induced lacZ mutation spectrum in transgenic mice using next-generation sequencing

Figure S1. Comparison of mutant read proportions for substitutions at each nucleotide position across all samples. Figure S2. Example density graphs (smoothed histograms) for variant calls at two different nucleotide positions. Figure S3. Distribution of read starts and ends. Figure S4. Comparison of the density of false mutation proportions between base substitutions (red) and indels (blue). Figure S5. Relative proportion of control and BaP-induced lacI mutations in liver from reference [29]. Figure S6. Bone marrow mutation spectra of control and BaP treatments. Figure S7. Comparison of spontaneous mutation spectra between our NGS dataset and other published datasets [4, 5, 7, 9-11]. Figure S8. Comparison of BaP-induced mutation spectrum in bone marrow measured using NGS with the mean mutation spectrum measured from four tissues (forestomach, spleen, colon, glandular stomach) using Sanger sequencing [6]. Figure S9. Distribution of non-unique base substitutions across the lacZ transgene for control and BaP samples. Figure S10. Comparison of lacZ mutation hotspots identified using Sanger sequencing [5-10] with mutations identified using NGS at the same nucleotide positions in the present study. Figure S11. Distribution of non-unique indels across the lacZ transgene for control and BaP samples. Figure S12. Results of simulations that use random sampling of BaP mutants to approximate the number of mutants per sample required to achieve a consistent mutation spectrum. Table S1. Thresholds used to detect mutations from each sample library. Table S2. Comparison of expected and observed mutant count when the number of each mutant plaque was controlled for in each NGS library. Table S3. Percent Clonality and Adjusted Mutant Frequencies in Control and BaP-treated samples using the LOD/linear model to adjust mutant counts. Table S4. Comparison of BaP-induced and spontaneous mutation spectra. (DOCX 418 kb)