Run ID: ERR1034882
Sample name:
Date: 20-10-2023 23:23:44
Number of reads: 18776962
Percentage reads mapped: 99.71
Strain: lineage4.3.4.2
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB c.1287_1295delGCTGAGCCA (1.00) |
| Isoniazid | R | fabG1 c.-15C>T (1.00), inhA p.Ser94Ala (1.00) |
| Ethambutol | ||
| Pyrazinamide | R | pncA c.-7T>C (0.40) |
| Streptomycin | R | rpsL p.Lys43Arg (1.00) |
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | R | fabG1 c.-15C>T (1.00), inhA p.Ser94Ala (1.00) |
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
| lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
| lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 1.0 |
| lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761087 | c.1287_1295delGCTGAGCCA | disruptive_inframe_deletion | 1.0 | rifampicin |
| rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
| fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
| inhA | 1674481 | p.Ser94Ala | missense_variant | 1.0 | isoniazid, ethionamide |
| pncA | 2289248 | c.-7T>C | upstream_gene_variant | 0.4 | pyrazinamide |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 6817 | c.-485G>A | upstream_gene_variant | 1.0 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.99 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 |
| clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
| embC | 4239763 | c.-100C>T | upstream_gene_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |
