Run ID: ERR1035274
Sample name:
Date: 2024-10-04T03:20:38.186683
Number of reads: 6770388
Percentage reads mapped: 99.56
Median coverage: 135.0
Strain: lineage4.6.4
Spoligotype:
Drug-resistance: Pre-XDR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.6 | Euro-American | None | 0.99 |
| lineage4.6.4 | Euro-American | None | 0.99 |
| lineage4 | Euro-American | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
| isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
| ethambutol | embB | p.Met306Val | Assoc w R | |
| pyrazinamide | pncA | p.Thr76Pro | Assoc w R | |
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | gyrA | p.Ala90Val | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
| ofloxacin | ||||
| levofloxacin | gyrA | p.Ala90Val | Assoc w R | |
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| gyrA | 7570 | p.Ala90Val | missense_variant | 0.92 | levofloxacin | Assoc w R | |
| moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| pncA | 2289016 | p.Thr76Pro | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
| embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| dnaA | 29 | p.Thr10Ser | missense_variant | 0.99 | isoniazid | Uncertain significance |
| 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| Rv0010c | 13569 | c.-11C>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
| rpoB | 762715 | p.Val970Ala | missense_variant | 0.99 | rifampicin | Uncertain significance |
| 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 |
| Rv1129c | 1254144 | p.Thr131Pro | missense_variant | 0.99 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1474750 | n.1093C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| inhA | 1674685 | p.Thr162Ala | missense_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.99 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| katG | 2156724 | c.-613C>T | upstream_gene_variant | 1.0 | isoniazid | |
| Rv1979c | 2222795 | p.Asp124Asn | missense_variant | 0.99 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| pncA | 2288792 | c.450C>T | synonymous_variant | 1.0 | pyrazinamide | |
| eis | 2714393 | p.Val314Leu | missense_variant | 0.99 | kanamycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| Rv2477c | 2783928 | p.Pro39Ser | missense_variant | 1.0 | kanamycin | Uncertain significance |
| levofloxacin | Uncertain significance | |||||
| moxifloxacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| ethambutol | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| fbiD | 3339073 | c.-45G>C | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| lpqB | 3625390 | c.-480C>T | upstream_gene_variant | 0.99 | rifampicin | |
| bedaquiline | ||||||
| rpoA | 3878745 | c.-238C>G | upstream_gene_variant | 1.0 | rifampicin | Uncertain significance |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ethA | 4326693 | p.Arg261Trp | missense_variant | 1.0 | ethionamide | Uncertain significance |
| whiB6 | 4338546 | c.-25G>C | upstream_gene_variant | 0.99 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| 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 | 4407946 | p.Leu86Pro | missense_variant | 0.99 | streptomycin | Uncertain significance |
