Table 2.
Efficacy of SNP calling using the consensus sequence or H37Rv as the reference genome by comparing the number of SNPs detected
| i) individual strains | |||
|---|---|---|---|
| Species | Strain | vs H37Rv | vs consensus sequence |
| M. tuberculosis | CCDC5079 | 632 | 198* |
| CCDC5180 | 378 | 70* | |
| CDC1551 | 543 | 41* | |
| CTRI-2 | 140 | 15* | |
| Erdman | 570 | 104* | |
| F11 | 343 | 129* | |
| H37Ra | 44 | 38* | |
| H37Rv | 12 | ||
| KZN605 | 16 | 9 | |
| KZN1435 | 12 | 2 | |
| KZN4207 | 26 | 0 | |
| RGTB327 | 1242 | 127* | |
| RGTB423 | 2410 | 145* | |
| M. bovis BCG | Mexico | 13 | 0 |
| Moreau RDJ | 136 | 22* | |
| Pasteur | 20 | 0 | |
| Tokyo 172 | 56 | 76* | |
| M. africanum | GMO41182 | 876 | 152* |
| M. canettii | CIPT 140010059 | 24425* | 560 |
| Total SNP found in only one strain | 31882 | 1700 | |
| ii) group comparison | |||
| four BCG strains | 1040 | 52* | |
| three KZN strains | 121 | 15 | |
| All SNP at least found in one strain | 37589 | 3429 | |
Based on SNP calls using MUMmer [58], the number of SNPs called uniquely in individual strains, and in groups of BCG and KZN strains, was determined. *The number of SNPs detected using the H37Rv and consensus sequences as reference were compared for each strain (i) or group of strains (ii) using Fisher's exact test, with significant differences indicated with asterisks (p < 0.0001).