Run ID: ERR2179808
Sample name:
Date: 2024-10-04T20:17:31.783809
Number of reads: 5206273
Percentage reads mapped: 96.21
Median coverage: 151.0
Strain: lineage4.5
Spoligotype:
Drug-resistance: Other
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.5 | Euro-American | RD122 | 0.99 |
| lineage4 | Euro-American | 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 | fbiD | c.-1790_*23137del | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| fbiD | 3337327 | c.-1790_*23137del | transcript_ablation | 0.9 | delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 5684 | p.Val149Ile | missense_variant | 0.98 | levofloxacin | |
| moxifloxacin | ||||||
| gyrB | 6247 | p.Lys336Asn | missense_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7892 | c.591G>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 8715 | p.Pro472Ser | missense_variant | 0.99 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| ccsA | 620029 | c.139C>T | synonymous_variant | 0.99 | kanamycin | Not assoc w R - Interim |
| capreomycin | Not assoc w R - Interim | |||||
| amikacin | Not assoc w R - Interim | |||||
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpR5 | 778244 | c.-746G>C | upstream_gene_variant | 0.99 | bedaquiline | |
| clofazimine | ||||||
| mmpS5 | 778614 | p.Ser98Ala | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| Rv1258c | 1406987 | c.354G>T | synonymous_variant | 1.0 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| bacA | 2046009 | c.-23424_*16799del | transcript_ablation | 0.93 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| PPE35 | 2164492 | c.1083_*3156del | frameshift_variant&stop_lost&splice_region_variant | 0.91 | pyrazinamide | Uncertain significance |
| PPE35 | 2170568 | p.Ile15Met | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 0.99 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| folC | 2744108 | c.-28182_*2026del | transcript_ablation | 0.93 | para-aminosalicylic_acid | |
| folC | 2747194 | c.-14689_404del | frameshift_variant&start_lost | 0.92 | para-aminosalicylic_acid | |
| Rv3083 | 3448478 | c.-25delG | upstream_gene_variant | 1.0 | ethionamide | Uncertain significance |
| Rv3236c | 3608504 | c.-23350_*3454del | transcript_ablation | 0.91 | pyrazinamide | Uncertain significance |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| alr | 3811305 | c.-13525_*28888del | transcript_ablation | 0.93 | cycloserine | |
| alr | 3835785 | c.-15543_*4408del | transcript_ablation | 0.9 | cycloserine | |
| rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
| clpC1 | 4038318 | p.Pro796Leu | missense_variant | 0.99 | pyrazinamide | Not assoc w R |
| embA | 4199607 | c.-43625_*2878del | transcript_ablation | 0.95 | ethambutol | Uncertain significance |
| embA | 4201096 | c.-42136_*2231del | transcript_ablation | 0.92 | ethambutol | Uncertain significance |
| embC | 4217305 | c.-22557_*44del | transcript_ablation | 0.92 | ethambutol | |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4245524 | c.-989_2246del | frameshift_variant&start_lost | 0.91 | ethambutol | |
| aftB | 4267931 | c.-7688_905del | frameshift_variant&start_lost | 0.93 | ethambutol | Uncertain significance |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| gid | 4407641 | p.Val188Leu | missense_variant | 1.0 | streptomycin |
