Run ID: ERR4829752
Sample name:
Date: 2024-04-16T07:26:47.505829
Number of reads: 2093193
Percentage reads mapped: 99.59
Median coverage: 63.0
Strain: lineage4.4.1.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.4.1 | Euro-American (S-type) | None | 1.0 |
| lineage4 | Euro-American | None | 1.0 |
| lineage4.4.1.1 | Euro-American | None | 1.0 |
| lineage4.4 | 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.Met306Ile | Assoc w R | |
| pyrazinamide | pncA | p.His57Pro | Uncertain significance | Mutation from literature |
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | gyrA | p.Asp94Gly | Assoc w R | High-level resistance |
| ofloxacin | ||||
| levofloxacin | gyrA | p.Asp94Gly | Assoc w R | |
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | eis | c.-15C>G | Uncertain significance | Mutation from literature |
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | moxifloxacin | Assoc w R | High-level resistance |
| levofloxacin | Assoc w R | ||||||
| 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 | 2289072 | p.His57Pro | missense_variant | 1.0 | pyrazinamide | Uncertain significance | Mutation from literature |
| eis | 2715347 | c.-15C>G | upstream_gene_variant | 1.0 | kanamycin | Uncertain significance | Mutation from literature |
| embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol | 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 | |||||
| mshA | 576108 | p.Ala254Gly | missense_variant | 0.28 | ethionamide | |
| isoniazid | ||||||
| rpoB | 761998 | p.Leu731Pro | missense_variant | 1.0 | rifampicin | Uncertain significance |
| rpoC | 766809 | p.Val1147Ala | missense_variant | 1.0 | rifampicin | Uncertain significance |
| 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 |
| Rv1258c | 1406392 | c.949T>C | synonymous_variant | 1.0 | streptomycin | |
| isoniazid | Not assoc w R - Interim | |||||
| pyrazinamide | ||||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.98 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rpsA | 1833626 | p.Thr29Ala | 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 | 2102990 | p.Val18Ala | missense_variant | 1.0 | ethionamide | Uncertain significance |
| delamanid | Uncertain significance | |||||
| isoniazid | Not assoc w R | |||||
| PPE35 | 2169840 | p.Gly258Asp | missense_variant | 1.0 | pyrazinamide | 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 | |||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3083 | 3448608 | c.105G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| Rv3083 | 3449909 | p.Asp469Gly | missense_variant | 1.0 | ethionamide | Uncertain significance |
| Rv3236c | 3612665 | p.Val151Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| alr | 3841433 | c.-13G>C | upstream_gene_variant | 1.0 | cycloserine | |
| glpK | 4139371 | p.Asp129Tyr | missense_variant | 0.64 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| glpK | 4139604 | p.Pro51Arg | missense_variant | 0.21 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| embC | 4238963 | c.-900C>T | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ethA | 4326287 | p.Asp396Gly | missense_variant | 1.0 | ethionamide | Uncertain significance |
| whiB6 | 4338204 | c.318G>T | synonymous_variant | 1.0 | capreomycin | |
| amikacin | Not assoc w R - Interim | |||||
| kanamycin | Not assoc w R - Interim | |||||
| 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 | 4408084 | p.Glu40Ala | missense_variant | 1.0 | streptomycin | Uncertain significance |
