Online Supplementary Figures of Chapter 3 Fabio Gori Figures 1-30 contain pie charts showing the population characterization re- sulting from the taxonomic assignment computed by the methods. On the simulated datasets the true population distribution is also shown. 1 MTR Bacillales (47.11%) Thermoanaerobacterales (0.76%) Clostridiales (33.58%) Lactobacillales (7.99%) Others (10.55%) LCA Bacillales (48.38%) Thermoanaerobacterales (0.57%) Clostridiales (32.14%) Lactobacillales (10.07%) Others (8.84%) True Distribution 333 386 Prochlorales (5.84%) 535 Bacillales (34.61%) Halanaerobiales (4.37%) Thermoanaerobacterales (10.29%) Clostridiales (28.75%) Lactobacillales (9.38%) 1974 Herpetosiphonales (6.77%) 1640 249 587 Figure 1: Population distributions (rank Order) of M1, coverage 0.1x, by MTR and LCA, and the true population distribution. 2 MTR Bacillus (47.34%) Clostridium (14.61%) Lactobacillus (8.71%) Anaerocellum (11.41%) Alkaliphilus (5.14%) Others (12.79%) LCA Bacillus (51.41%) Clostridium (8.08%) Lactobacillus (9.23%) Anaerocellum (15.79%) Alkaliphilus (5.17%) Others (10.31%) True Distribution 386 552 Herpetosiphon (6.77%) 333 Prochlorococcus (5.84%) 587 Bacillus (34.61%) Clostridium (19.07%) Lactobacillus (9.38%) 249 Halothermothrix (4.37%) Caldicellulosiruptor (10.29%) Alkaliphilus (9.68%) 535 1974 1088 Figure 2: Population distributions (rank Genus) of M1, coverage 0.1x, by MTR and LCA, and the true population distribution. 3 MTR Prochlorales (0.07%) Bacillales (47.97%) Thermoanaerobacterales (0.66%) Clostridiales (32.18%) Lactobacillales (7.76%) Others (11.35%) LCA Prochlorales (0.10%) Bacillales (49.02%) Thermoanaerobacterales (0.59%) Clostridiales (30.62%) Lactobacillales (9.50%) Others (10.16%) True Distribution 3293 3950 Prochlorales (5.65%) 5263 Bacillales (36.68%) Halanaerobiales (3.98%) Thermoanaerobacterales (10.56%) Clostridiales (27.34%) Lactobacillales (9.03%) 21382 Herpetosiphonales (6.78%) 15936 2320 6154 Figure 3: Population distributions (rank Order) of M1, coverage 1x, by MTR and LCA, and the true population distribution. 4 MTR Prochlorococcus (0.08%) Bacillus (47.02%) Clostridium (12.39%) Lactobacillus (7.34%) Anaerocellum (11.64%) Caldicellulosiruptor (0.01%) Alkaliphilus (5.17%) Others (16.35%) LCA Prochlorococcus (0.13%) Bacillus (50.58%) Clostridium (7.84%) Lactobacillus (7.96%) Anaerocellum (15.14%) Caldicellulosiruptor (0.02%) Alkaliphilus (4.58%) Others (13.74%) True Distribution 3950 5536 Herpetosiphon (6.78%) 3293 Prochlorococcus (5.65%) 6154 Bacillus (36.68%) Clostridium (17.84%) Lactobacillus (9.03%) 2320 Halothermothrix (3.98%) Caldicellulosiruptor (10.56%) Alkaliphilus (9.50%) 5263 21382 10400 Figure 4: Population distributions (rank Genus) of M1, coverage 1x, by MTR and LCA, and the true population distribution. 5 MTR Chroococcales (5.33%) Prochlorales (0.08%) Bacillales (55.35%) Thermoanaerobacterales (0.76%) Clostridiales (32.40%) Others (6.07%) LCA Chroococcales (3.89%) Prochlorales (0.11%) Bacillales (58.88%) Thermoanaerobacterales (0.58%) Clostridiales (30.25%) Others (6.28%) True Distribution 13242 8576 Prochlorales (7.47%) Bacillales (46.46%) Halanaerobiales (4.91%) 41237 Thermoanaerobacterales (13.04%) Clostridiales (23.27%) Herpetosiphonales (4.84%) 82311 23108 8704 Figure 5: Population distributions (rank Order) of M1, coverage 4x, by MTR and LCA, and the true population distribution. 6 MTR Synechococcus (5.03%) Prochlorococcus (0.09%) Bacillus (53.14%) Clostridium (7.44%) Anaerocellum (14.57%) Caldicellulosiruptor (0.02%) Alkaliphilus (6.60%) Others (13.11%) LCA Synechococcus (3.08%) Prochlorococcus (0.14%) Bacillus (59.89%) Clostridium (4.02%) Anaerocellum (17.51%) Caldicellulosiruptor (0.03%) Alkaliphilus (5.36%) Others (9.97%) True Distribution 8576 22256 13242 Herpetosiphon (4.84%) Prochlorococcus (7.47%) Bacillus (46.46%) Clostridium (10.71%) 23108 Halothermothrix (4.91%) Caldicellulosiruptor (13.04%) Alkaliphilus (12.56%) 8704 82311 18981 Figure 6: Population distributions (rank Genus) of M1, coverage 4x, by MTR and LCA, and the true population distribution. 7 MTR Malpighiales (4.26%) Desulfuromonadales (19.45%) Burkholderiales (72.56%) Others (3.73%) LCA Malpighiales (5.61%) Desulfuromonadales (22.01%) Burkholderiales (68.01%) Others (4.36%) True Distribution Desulfuromonadales (21.87%) 1984 Burkholderiales (78.13%) 7086 Figure 7: Population distributions (rank Order) of M2, coverage 0.1x, by MTR and LCA, and the true population distribution. 8 MTR Comamonas (0.09%) Populus (5.40%) Acidovorax (15.57%) Geobacter (18.70%) Burkholderia (49.23%) Others (11.00%) LCA Comamonas (0.15%) Populus (7.58%) Acidovorax (3.46%) Geobacter (19.96%) Burkholderia (57.46%) Others (11.39%) True Distribution 1415 Comamonas (15.60%) 1991 Geobacter (21.87%) Burkholderia (40.57%) Delftia (21.95%) 1984 3680 Figure 8: Population distributions (rank Genus) of M2, coverage 0.1x, by MTR and LCA, and the true population distribution. 9 MTR Malpighiales (4.60%) Desulfuromonadales (19.34%) Burkholderiales (71.18%) Others (4.89%) LCA Malpighiales (6.00%) Desulfuromonadales (21.22%) Burkholderiales (67.31%) Others (5.47%) True Distribution Desulfuromonadales (22.09%) 20375 Burkholderiales (77.91%) 71882 Figure 9: Population distributions (rank Order) of M2, coverage 1x, by MTR and LCA, and the true population distribution. 10 MTR Comamonas (0.11%) Populus (4.76%) Acidovorax (14.06%) Geobacter (18.36%) Burkholderia (49.82%) Delftia (0.04%) Others (12.84%) LCA Comamonas (0.18%) Populus (7.79%) Acidovorax (3.25%) Geobacter (19.05%) Burkholderia (56.15%) Delftia (0.08%) Others (13.51%) True Distribution 14357 Comamonas (15.56%) 20341 Geobacter (22.09%) Burkholderia (40.30%) Delftia (22.05%) 20375 37184 Figure 10: Population distributions (rank Genus) of M2, coverage 1x, by MTR and LCA, and the true population distribution. 11 MTR Malpighiales (8.05%) Desulfuromonadales (2.21%) Burkholderiales (84.30%) Others (5.44%) LCA Malpighiales (10.29%) Desulfuromonadales (2.21%) Burkholderiales (80.83%) Others (6.67%) True Distribution 4852 Desulfuromonadales (2.77%) Burkholderiales (97.23%) 170140 Figure 11: Population distributions (rank Order) of M2, coverage 4x, by MTR and LCA, and the true population distribution. 12 MTR Populus (8.48%) Acidovorax (15.11%) Geobacter (0.83%) Burkholderia (61.36%) Delftia (0.06%) Others (14.16%) LCA Populus (12.92%) Acidovorax (3.34%) Geobacter (1.16%) Burkholderia (69.24%) Delftia (0.10%) Others (13.25%) True Distribution 4852 Geobacter (2.77%) Burkholderia (53.14%) Delftia (44.08%) 77141 92999 Figure 12: Population distributions (rank Genus) of M2, coverage 4x, by MTR and LCA, and the true population distribution. 13 MTR Rhizobiales (2.92%) Pseudomonadales (21.51%) Bifidobacteriales (8.27%) Chromatiales (0.06%) Xanthomonadales (17.72%) Alteromonadales (46.09%) Others (3.42%) LCA Rhizobiales (0.85%) Pseudomonadales (18.94%) Bifidobacteriales (10.18%) Chromatiales (0.09%) Xanthomonadales (21.34%) Alteromonadales (45.62%) Others (2.98%) True Distribution 745 Rhizobiales (6.30%) Pseudomonadales (21.74%) Bifidobacteriales (8.52%) 2571 Chromatiales (0.09%) Xanthomonadales (19.18%) 5222 Alteromonadales (44.16%) 1007 11 2268 Figure 13: Population distributions (rank Order) of M3, coverage 0.1x, by MTR and LCA, and the true population distribution. 14 MTR Shewanella (48.41%) Pseudomonas (20.79%) Bifidobacterium (8.86%) Stenotrophomonas (18.26%) Others (3.69%) LCA Shewanella (50.16%) Pseudomonas (18.58%) Bifidobacterium (11.75%) Stenotrophomonas (17.25%) Others (2.25%) True Distribution 745 11 Shewanella (44.16%) Pseudomonas (21.74%) Bifidobacterium (8.52%) 2268 Stenotrophomonas (19.18%) Halorhodospira (0.09%) 5222 Parvibaculum (6.30%) 1007 2571 Figure 14: Population distributions (rank Genus) of M3, coverage 0.1x, by MTR and LCA, and the true population distribution. 15 MTR Rhizobiales (2.46%) Pseudomonadales (21.21%) Bifidobacteriales (8.11%) Chromatiales (0.09%) Xanthomonadales (18.07%) Alteromonadales (46.32%) Others (3.73%) LCA Rhizobiales (0.82%) Pseudomonadales (17.88%) Bifidobacteriales (9.97%) Chromatiales (0.12%) Xanthomonadales (22.00%) Alteromonadales (46.20%) Others (3.02%) True Distribution 6650 Rhizobiales (5.69%) Pseudomonadales (21.32%) Bifidobacteriales (8.35%) 24939 Chromatiales (0.12%) Xanthomonadales (19.61%) Alteromonadales (44.91%) 52521 9771 139 22929 Figure 15: Population distributions (rank Order) of M3, coverage 1x, by MTR and LCA, and the true population distribution. 16 MTR Shewanella (46.50%) Pseudomonas (20.64%) Bifidobacterium (8.60%) Stenotrophomonas (18.56%) Parvibaculum (0.01%) Others (5.70%) LCA Shewanella (49.93%) Pseudomonas (17.44%) Bifidobacterium (11.30%) Stenotrophomonas (17.49%) Parvibaculum (0.01%) Others (3.83%) True Distribution 6650 139 Shewanella (44.91%) Pseudomonas (21.32%) Bifidobacterium (8.35%) 22929 Stenotrophomonas (19.61%) Halorhodospira (0.12%) Parvibaculum (5.69%) 52521 9771 24939 Figure 16: Population distributions (rank Genus) of M3, coverage 1x, by MTR and LCA, and the true population distribution. 17 MTR Bifidobacteriales (0.66%) Alteromonadales (97.01%) Others (2.33%) LCA Bifidobacteriales (0.79%) Alteromonadales (97.35%) Others (1.86%) True Distribution 1157 Bifidobacteriales (0.69%) Alteromonadales (99.31%) 165819 Figure 17: Population distributions (rank Order) of M3, coverage 4x, by MTR and LCA, and the true population distribution. 18 MTR Shewanella (96.71%) Bifidobacterium (0.70%) Others (2.58%) LCA Shewanella (97.52%) Bifidobacterium (0.83%) Others (1.65%) True Distribution 1157 Shewanella (99.31%) Bifidobacterium