Run ID: SRR20969632
Sample name:
Date: 2024-10-04T19:36:32.737980
Number of reads: 8020382
Percentage reads mapped: 99.61
Median coverage: 223.0
Strain: lineage4.5
Spoligotype:
Drug-resistance: Other
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.5 | Euro-American | RD122 | 1.0 |
| 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 | mmpR5 | c.42dupC | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | mmpR5 | c.42dupC | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| mmpR5 | 779028 | c.42dupC | frameshift_variant | 1.0 | bedaquiline | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
| clofazimine | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| ccsA | 620029 | c.139C>T | synonymous_variant | 1.0 | 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 | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rplC | 801126 | c.318C>T | synonymous_variant | 1.0 | linezolid | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472048 | n.205delG | non_coding_transcript_exon_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rpsA | 1833832 | p.Glu97Asp | missense_variant | 1.0 | pyrazinamide | |
| 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 |
| ndh | 2103141 | c.-99T>C | upstream_gene_variant | 1.0 | isoniazid | |
| delamanid | ||||||
| ethionamide | ||||||
| PPE35 | 2170568 | p.Ile15Met | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| folC | 2746579 | c.1020G>A | synonymous_variant | 1.0 | para-aminosalicylic_acid | |
| fbiD | 3339452 | p.Val112Ala | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| alr | 3841546 | c.-126C>A | upstream_gene_variant | 1.0 | cycloserine | |
| alr | 3841589 | c.-170delG | upstream_gene_variant | 1.0 | cycloserine | |
| alr | 3841612 | c.-193_-192insC | upstream_gene_variant | 0.99 | cycloserine | |
| rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
| clpC1 | 4038318 | p.Pro796Leu | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| embC | 4239859 | c.-4C>T | upstream_gene_variant | 1.0 | ethambutol | |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| aftB | 4268596 | p.Tyr81His | missense_variant | 1.0 | ethambutol | Uncertain significance |
| whiB6 | 4338337 | c.184_185insA | frameshift_variant&stop_gained | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| amikacin | 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 |
