Run ID: ERR775363
Sample name:
Date: 2024-03-24T16:18:55.884106
Number of reads: 4190631
Percentage reads mapped: 99.49
Median coverage: 93.0
Strain: lineage4.1.2
Spoligotype:
Drug-resistance: MDR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.1 | Euro-American | None | 1.0 |
| lineage4.1.2 | Euro-American | None | 1.0 |
| 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.Asp354Ala | Assoc w R | |
| pyrazinamide | pncA | c.-11A>G | Assoc w R | |
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ethA | c.480_*217del | Assoc w R | |
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| 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 | 2289252 | c.-11A>G | upstream_gene_variant | 1.0 | pyrazinamide | Assoc w R | |
| embB | 4247574 | p.Asp354Ala | missense_variant | 1.0 | ethambutol | Assoc w R | |
| ethA | 4325786 | c.480_*217del | frameshift_variant&stop_lost&splice_region_variant | 0.98 | ethionamide | Assoc w R |
| 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| fgd1 | 491591 | p.Lys270Met | missense_variant | 1.0 | clofazimine | Not assoc w R |
| pretomanid | ||||||
| delamanid | Uncertain significance | |||||
| mshA | 575440 | c.93C>G | synonymous_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
| rpoB | 760115 | c.309C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 765150 | p.Gly594Glu | missense_variant | 0.99 | rifampicin | Not assoc w R |
| mmpL5 | 775639 | p.Ile948Val | 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 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rpsA | 1834262 | p.Ser241Thr | 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 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 | isoniazid | |
| Rv2477c | 2782763 | p.Ser427Leu | missense_variant | 1.0 | ethambutol | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| streptomycin | ||||||
| levofloxacin | Uncertain significance | |||||
| kanamycin | ||||||
| rifampicin | Uncertain significance | |||||
| amikacin | ||||||
| pepQ | 2860147 | p.Gly91Asp | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| Rv2680 | 2996085 | c.-20G>A | upstream_gene_variant | 0.24 | capreomycin | Uncertain significance |
| Rv2752c | 3066624 | c.-433C>T | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| rpoA | 3877960 | p.Val183Gly | missense_variant | 1.0 | rifampicin | Uncertain significance |
| clpC1 | 4038335 | c.2370C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242803 | p.Val981Leu | missense_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269308 | p.Phe176Leu | missense_variant | 0.99 | ethambutol | Uncertain significance |
| whiB6 | 4338440 | c.81dupT | frameshift_variant | 0.99 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| 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 | ||||||
| gid | 4408057 | p.Leu49Arg | missense_variant | 0.99 | streptomycin | Uncertain significance |
