Run ID: ERR775385
Sample name:
Date: 2024-03-24T16:18:56.975638
Number of reads: 4221088
Percentage reads mapped: 99.54
Median coverage: 92.0
Strain: lineage4.1.1.3
Spoligotype:
Drug-resistance: Pre-XDR-TB
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.1 | Euro-American | None | 1.0 |
| lineage4.1.1.3 | Euro-American (X-type) | RD193 | 1.0 |
| 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.Ser450Leu | Assoc w R | |
| isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
| ethambutol | embB | p.Gly406Ala | Assoc w R | |
| pyrazinamide | pncA | p.Met175Val | Assoc w R | |
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | gyrA | p.Asp94Asn | Assoc w R | High-level resistance |
| ofloxacin | ||||
| levofloxacin | gyrA | p.Asp94Asn | 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 | 7581 | p.Asp94Asn | missense_variant | 0.99 | 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 | 2288719 | p.Met175Val | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
| embB | 4247730 | p.Gly406Ala | missense_variant | 0.99 | 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 | |||||
| Rv0010c | 13452 | p.Gly36Val | missense_variant | 0.99 | isoniazid | Uncertain significance |
| Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
| rpoC | 764817 | p.Val483Ala | missense_variant | 1.0 | rifampicin | 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 | |
| fbiC | 1302954 | c.24G>A | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
| pretomanid | ||||||
| delamanid | Not assoc w R - Interim | |||||
| 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 |
| tlyA | 1918623 | p.Ser228Arg | missense_variant | 1.0 | capreomycin | Uncertain significance |
| katG | 2154678 | c.1434G>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| PPE35 | 2169405 | p.Asn403Ser | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| ahpC | 2726409 | p.Asp73His | missense_variant | 1.0 | isoniazid | Uncertain significance |
| thyX | 3067949 | c.-4C>G | upstream_gene_variant | 0.99 | para-aminosalicylic_acid | |
| thyA | 3074197 | p.Pro92Leu | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ald | 3086232 | c.-587_815del | frameshift_variant&start_lost | 0.97 | cycloserine | |
| Rv3083 | 3449437 | c.936_942delCGCGGCG | frameshift_variant | 1.0 | ethionamide | Uncertain significance |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| fbiA | 3640330 | c.-213C>T | upstream_gene_variant | 0.99 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| 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 | 4249408 | c.2895G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4249678 | c.3165C>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| ubiA | 4269671 | p.Val55Leu | missense_variant | 1.0 | ethambutol | Uncertain significance |
| ethA | 4326353 | p.Leu374Arg | missense_variant | 1.0 | ethionamide | Uncertain significance |
| whiB6 | 4338594 | c.-73T>A | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| 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 | 4407934 | p.Leu90Arg | missense_variant | 1.0 | streptomycin | Uncertain significance |
