Run ID: SRR10993937
Sample name:
Date: 2024-04-16T00:41:30.850415
Number of reads: 265901
Percentage reads mapped: 99.47
Median coverage: 9.0
Strain: La1.6
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| La1.6 | M.bovis | None | 1.0 |
| La1 | M.bovis | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| dnaA | 467 | p.His156Arg | missense_variant | 1.0 | isoniazid | Not assoc w R |
| gyrB | 5752 | c.513G>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 8285 | c.984C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| Rv0010c | 13197 | p.Thr121Ser | missense_variant | 1.0 | isoniazid | Not assoc w R |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
| pretomanid | ||||||
| delamanid | Not assoc w R - Interim | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
| rrl | 1476022 | n.2365A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rpsA | 1834859 | p.Ala440Thr | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| tsnR | 1854289 | c.684C>T | synonymous_variant | 1.0 | linezolid | |
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| ndh | 2103142 | c.-100A>G | upstream_gene_variant | 1.0 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| ndh | 2103173 | c.-132delG | upstream_gene_variant | 1.0 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| katG | 2155503 | c.609C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| katG | 2156025 | c.87C>A | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| katG | 2156367 | c.-256G>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
| PPE35 | 2168814 | c.1798dupA | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| folC | 2746245 | p.Ala452Thr | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ribD | 2987615 | c.777A>G | stop_lost&splice_region_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2681 | 2997325 | p.Ala196Val | missense_variant | 1.0 | capreomycin | Uncertain significance |
| ald | 3086728 | c.-92C>T | upstream_gene_variant | 1.0 | cycloserine | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| clpC1 | 4038403 | c.2302T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| embA | 4244220 | c.988C>T | synonymous_variant | 0.92 | ethambutol | Not assoc w R |
| embB | 4246864 | c.351C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269351 | c.483C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin |
