Run ID: ERR4872182
Sample name:
Date: 2024-04-16T10:02:14.738152
Number of reads: 11768845
Percentage reads mapped: 98.68
Median coverage: 143.0
Strain: lineage4.1.1.1
Spoligotype:
Drug-resistance: MDR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.1 | Euro-American | None | 1.0 |
| lineage4.1.1.1 | Euro-American (X-type) | RD183 | 0.96 |
| lineage4 | Euro-American | None | 1.0 |
| lineage4.1.1 | Euro-American (X-type) | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | rpoB | p.His445Leu | Assoc w R | |
| p.Ala451Val | Assoc w R - Interim | |||
| isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
| ethambutol | embA | c.-12C>T | Uncertain significance | Mutation from literature |
| pyrazinamide | pncA | p.Gln122* | Assoc w R | |
| streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ethA | p.Leu272Pro | Uncertain significance | Mutation from literature |
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| rpoB | 761140 | p.His445Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
| rpoB | 761158 | p.Ala451Val | missense_variant | 1.0 | rifampicin | Assoc w R - Interim | |
| rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
| pncA | 2288878 | p.Gln122* | stop_gained | 1.0 | pyrazinamide | Assoc w R | |
| embA | 4243221 | c.-12C>T | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance | Mutation from literature |
| ethA | 4326659 | p.Leu272Pro | missense_variant | 1.0 | ethionamide | Uncertain significance | Mutation from literature |
| 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 | |||||
| Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.98 | ethionamide | Uncertain significance |
| rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | 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 |
| rplC | 800219 | c.-590T>C | upstream_gene_variant | 1.0 | linezolid | |
| Rv1129c | 1254635 | c.-101C>T | upstream_gene_variant | 0.99 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | ||||||
| isoniazid | ||||||
| embR | 1416222 | p.Phe376Leu | missense_variant | 0.1 | ethambutol | Not assoc w R |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| 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 |
| katG | 2154939 | p.Glu391Asp | missense_variant | 1.0 | isoniazid | Uncertain significance |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| ahpC | 2726210 | c.18T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| Rv2477c | 2784617 | c.-575T>C | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3083 | 3448478 | c.-25delG | upstream_gene_variant | 1.0 | ethionamide | Uncertain significance |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| fbiA | 3641447 | p.Thr302Met | missense_variant | 1.0 | clofazimine | Not assoc w R |
| pretomanid | ||||||
| delamanid | Uncertain significance | |||||
| rpoA | 3877553 | p.Glu319Lys | missense_variant | 1.0 | rifampicin | Not assoc w R |
| embC | 4240897 | c.1035C>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| 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 |
| embB | 4248024 | p.Glu504Gly | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269298 | p.Ile179Thr | missense_variant | 1.0 | ethambutol | Uncertain significance |
| whiB6 | 4338498 | p.Glu8Asp | missense_variant | 1.0 | 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 | 0.99 | capreomycin | |
| amikacin | ||||||
| kanamycin |
