Table 1 Detection of artificially mixed infections using the number of heterozygous SNPs and Bayesian model-based clustering analysis methods. Strain information, known mixture proportions and average coverage across the genome are also shown. The number of heterozygous SNPs in each sample is presented with the total number of different distinct coding and non-coding regions in which the SNPs are present
From: Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data
Sample information | Heterozygous sites to total SNP proportion | Bayesian model-based clustering | |||||||
|---|---|---|---|---|---|---|---|---|---|
Sample identifier | Major strain proportion | Major/minor strain lineage | Major/minor strain spoligotype | Average coverage | No. heterozygous SNPs (Total no. gene regions) | No. total SNPs | Proportion het-total SNPs (%) | No. of strains | Major strain proportion |
ERR221663 | 0.7 | 1/3 | EAI6-BGD1/CAS1-Kili | 183 | 1789 (1382) | 2372 | 75.4 | 2 | 0.64 |
ERR221662 | 0.7 | 3/1 | CAS1-Kili/EAI6-BGD1 | 176 | 1788 (1381) | 2373 | 75.3 | 2 | 0.72 |
ERR221641 | 0.7 | 4/3 | CAS1-Delhi/LAM11-ZWE | 179 | 1055 (912) | 1443 | 73.1 | 2 | 0.68 |
ERR221643 | 0.7 | 3/4 | LAM11-ZWE/CAS1-Delhi | 157 | 1051 (912) | 1437 | 73.1 | 2 | 0.69 |
ERR221656 | 0.7 | 2/4 | Beijing/LAM11-ZWE | 179 | 1046 (906) | 1426 | 73.4 | 2 | 0.69 |
ERR221659 | 0.7 | 4/2 | LAM11-ZWE/Beijing | 196 | 1042 (906) | 1415 | 73.6 | 2 | 0.71 |
ERR221623 | 0.7 | 1/1 | EAI1-SOM/EAI6-BGD1 | 172 | 988 (848) | 2271 | 43.5 | 2 | 0.73 |
ERR221627 | 0.7 | 1/1 | EAI6-BGD1/EAI1-SOM | 189 | 985 (845) | 2269 | 43.4 | 2 | 0.65 |
ERR221647 | 0.7 | 4/4 | LAM11-ZWE/T | 223 | 640 (571) | 784 | 81.6 | 2 | 0.72 |
ERR221651 | 0.7 | 4/4 | T/LAM11-ZWE | 175 | 636 (567) | 779 | 81.6 | 2 | 0.67 |
ERR221630 | 0.7 | 2/2 | Beijing/Beijing | 168 | 186 (181) | 1212 | 15.3 | 2 | 0.67 |
ERR221628 | 0.7 | 2/2 | Beijing/Beijing | 191 | 183 (178) | 1212 | 15.1 | 2 | 0.69 |
ERR221660 | 0.9 | 1/3 | EAI6-BGD1/CAS1-Kili | 211 | 617 (550) | 1932 | 31.9 | 2 | 0.85 |
ERR221620 | 0.9 | 1/1 | EAI6-BGD1/EAI1-SOM | 173 | 571 (520) | 1994 | 28.6 | 2 | 0.85 |
ERR221636 | 0.9 | 3/4 | LAM11-ZWE/CAS1-Delhi | 155 | 316 (299) | 893 | 35.4 | 2 | 0.86 |
ERR221665 | 0.9 | 3/1 | CAS1-Kili/EAI6-BGD1 | 151 | 232 (218) | 1299 | 17.9 | 2 | 0.87 |
ERR221640 | 0.9 | 4/3 | CAS1-Delhi/LAM11-ZWE | 162 | 169 (155) | 1175 | 14.4 | 2 | 0.87 |
ERR221654 | 0.9 | 4/2 | LAM11-ZWE/Beijing | 205 | 165 (156) | 772 | 21.4 | 2 | 0.86 |
ERR221644 | 0.9 | 4/4 | T/LAM11-ZWE | 181 | 150 (143) | 360 | 41.7 | 2 | 0.86 |
ERR221625 | 0.9 | 1/1 | EAI1-SOM/EAI6-BGD1 | 168 | 147 (141) | 1814 | 8.1 | 2 | 0.86 |
ERR221652 | 0.9 | 2/4 | Beijing/LAM11-ZWE | 192 | 138 (130) | 1139 | 12.1 | 2 | 0.86 |
ERR221634 | 0.9 | 2/2 | Beijing/Beijing | 177 | 72 (69) | 1137 | 6.3 | 2 | 0.85 |
ERR221629 | 0.9 | 2/2 | Beijing/Beijing | 170 | 55 (55) | 1130 | 4.9 | 2 | 0.86 |
ERR221649 | 0.9 | 4/4 | LAM11-ZWE/T | 169 | 12 (10) | 687 | 1.7 | 1 | 1 |
ERR221635 | 0.95 | 2/2 | Beijing/Beijing | 193 | 609 (535) | 1162 | 52.4 | 2 | 0.83 |
ERR221632 | 0.95 | 2/2 | Beijing/Beijing | 196 | 186 (177) | 1136 | 16.4 | 2 | 0.85 |
ERR221653 | 0.95 | 4/2 | LAM11-ZWE/Beijing | 170 | 20 (16) | 699 | 2.9 | 1 | 1.00 |
ERR221650 | 0.95 | 4/4 | LAM11-ZWE/T | 174 | 18 (18) | 691 | 2.6 | 1 | 1.00 |
ERR221637 | 0.95 | 4/3 | CAS1-Delhi/LAM11-ZWE | 156 | 29 (19) | 1148 | 2.5 | 1 | 1.00 |
ERR221645 | 0.95 | 4/4 | T/LAM11-ZWE | 200 | 6 (4) | 241 | 2.5 | 1 | 1.00 |
ERR221655 | 0.95 | 2/4 | Beijing/LAM11-ZWE | 193 | 20 (17) | 1117 | 1.8 | 2 | 0.87 |
ERR221664 | 0.95 | 3/1 | CAS1-Kili/EAI6-BGD1 | 166 | 18 (9) | 1185 | 1.5 | 1 | 1.00 |
ERR221666 | 0.95 | 1/3 | EAI6-BGD1/CAS1-Kili | 157 | 25 (20) | 1774 | 1.4 | 2 | 0.91 |
ERR221626 | 0.95 | 1/1 | EAI1-SOM/EAI6-BGD1 | 189 | 20 (18) | 1766 | 1.1 | 1 | 1.00 |
ERR221638 | 0.95 | 3/4 | LAM11-ZWE/CAS1-Delhi | 161 | 6 (6) | 678 | 0.9 | 1 | 1.00 |
ERR221621 | 0.95 | 1/1 | EAI6-BGD1/EAI1-SOM | 174 | 12 (11) | 1792 | 0.7 | 1 | 1.00 |
ERR221646 | 1.00 | 4 | T | 165 | 4 (2) | 242 | 1.7 | 1 | 1.00 |
ERR221642 | 1.00 | 4 | CAS1-Delhi | 170 | 12 (5) | 1144 | 1.1 | 1 | 1.00 |
ERR221624 | 1.00 | 1 | EAI1-SOM | 187 | 18 (7) | 1765 | 1.0 | 1 | 1.00 |
ERR221648 | 1.00 | 4 | LAM11-ZWE | 190 | 7 (6) | 685 | 1.0 | 1 | 1.00 |
ERR221657 | 1.00 | 4 | LAM11-ZWE | 173 | 7 (5) | 687 | 1.0 | 1 | 1.00 |
ERR221661 | 1.00 | 3 | CAS1-Kili | 178 | 11 (7) | 1185 | 0.9 | 1 | 1.00 |
ERR221633 | 1.00 | 2 | Beijing | 171 | 5 (5) | 1110 | 0.5 | 1 | 1.00 |
ERR221658 | 1.00 | 2 | Beijing | 185 | 5 (5) | 1113 | 0.5 | 1 | 1.00 |
ERR221631 | 1.00 | 2 | Beijing | 151 | 5 (5) | 1129 | 0.4 | 1 | 1.00 |
ERR221639 | 1.00 | 3 | LAM11-ZWE | 147 | 2 (2) | 671 | 0.3 | 1 | 1.00 |
ERR221667 | 1.00 | 1 | EAI6-BGD1 | 180 | 4 (3) | 1769 | 0.2 | 1 | 1.00 |
ERR221622 | 1.00 | 1 | EAI6-BGD1 | 187 | 3 (3) | 1789 | 0.2 | 1 | 1.00 |