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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
  1. The samples are ordered by the known major strain proportion and then by number of heterozygous sites. Samples identified as mixed infections are shown in bold