Table 3. Resistance determinants found by the four methods for M. tuberculosis streptomycin resistance.
| Legend | resistome-based | DBGWAS | pyseer | HAWK |
| Time (mem) | 1h31m (2.1 GB) | 42m (4.3 GB) | 14h14m (102.4 GB) | 3h01m (3.7 GB) |
| Nb reported | 28 variants | 24 subgraphs | 85,011 k-mers | 2,038 reassembled k-mers |
| Known positive |
rpsL (1.96 × 10−33) | rpsL (3.70 × 10−31) | rpsL (4.85 × 10−55) | rpsL (5.72 × 10−47) |
| rrs (5.40 × 10−8) | rrs (2.86 × 10−9) | rrs (1.63 × 10−14) | rrs (3.45 × 10−20) | |
| Determinant described for other antibiotics | katG (2.61 × 10−30) | katG (1.06 × 10−28) | katG (2.12 × 10−71) | katG (1.44 × 10−57) |
| rpoB | rpoB | rpoB | embB | |
| gidB | embB | embB | kasA | |
| gyrA | gyrA | ubiA | embC | |
| embB | gidB | pncA | gyrA | |
| fabG1 promoter | rpoC | fabG1 promoter | iniA | |
| pncA | fabG1 promoter | gyrA | embA | |
| rpoC | ubiA | gidB | embR | |
| inhA | ethA | gidB | ||
| embA | tsnR | |||
| embC | rpoB | |||
| pncA | ||||
| ethA | ||||
| Unknown (top list) |
espG1 (1.20 × 10−3) | NC near tnp/PE (1.13 × 10−19) | NC near tnp/PPE (2.93 × 10−57) | |
| rpsN | Rv0270 | tnp | ||
| NC near tnp/PPE | Rv2665 | Rv2825c/Rv2828c | ||
| rnj | Rv2743c | 13E12 repeat family protein | ||
| Rv2672 | Rv2522c | PPE | ||
| espA promoter | NC near tnp/PPE | CRISPR repeats, down Cas genes | ||
| Rv2456c promoter | guaA | mmpL14 | ||
| whiB6 | kdpD | esxM | ||
| … | … | … |
This table presents the annotation of the features identified by the tested methods with default parameters. The total number of reported features, as well as the execution time and memory load (in Gigabytes) are given in the header. For k-mer-based methods, annotations were retrieved by mapping unitig/k-mer sequences to the resistance and Uniprot databases (see Interpretation of significant unitigs (step 3) subsection of the Methods section), and completed when needed by Blast on NCBI Nucleotide database. Green cells correspond to resistance determinants already described in the literature, orange cells to resistance determinants described for association with other antibiotics. The annotations not found by the resistome-based strategy are written in bold. Grey cells represent unknown determinants. Within each category, annotations are ordered by increasing minimum p/q-values. p/q-values are reported only for the most significant annotations. For each method, the annotation with the lowest p/q-values is underlined. ‘NC’ means noncoding region, ‘tnp’ transposase, ‘PE’ stands for PE-family protein and ‘PPE’ for PPE-family protein.