Run ID: ERR4829061
Sample name:
Date: 20-10-2023 07:14:52
Number of reads: 3996650
Percentage reads mapped: 99.57
Strain: lineage4.6.2.2
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Phe (1.00) |
| Isoniazid | R | katG p.Ser315Thr (1.00) |
| Ethambutol | R | embA c.-12C>T (1.00) |
| Pyrazinamide | ||
| Streptomycin | ||
| Fluoroquinolones | R | gyrA p.Asp94Ala (1.00) |
| Moxifloxacin | R | gyrA p.Asp94Ala (1.00) |
| Ofloxacin | R | gyrA p.Asp94Ala (1.00) |
| Levofloxacin | R | gyrA p.Asp94Ala (1.00) |
| Ciprofloxacin | R | gyrA p.Asp94Ala (1.00) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | ||
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
| lineage4.6 | Euro-American | T;LAM | None | 1.0 |
| lineage4.6.2 | Euro-American | T;LAM | RD726 | 1.0 |
| lineage4.6.2.2 | Euro-American (Cameroon) | LAM10-CAM | RD726 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Ala | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Phe | missense_variant | 1.0 | rifampicin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| embA | 4243221 | c.-12C>T | upstream_gene_variant | 1.0 | ethambutol |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpR5 | 778298 | c.-692C>T | upstream_gene_variant | 0.98 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| inhA | 1673393 | c.-809G>C | upstream_gene_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| Rv1979c | 2221746 | c.1416_1418dupCCG | disruptive_inframe_insertion | 0.99 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| Rv3083 | 3448567 | p.His22Asp | missense_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| ddn | 3987011 | c.168C>T | synonymous_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embB | 4248075 | p.Glu521Ala | missense_variant | 1.0 |
| aftB | 4267272 | p.Lys522Arg | missense_variant | 0.98 |
| ethR | 4326739 | c.-810G>C | upstream_gene_variant | 1.0 |
| ethA | 4326855 | p.Arg207Cys | missense_variant | 1.0 |
| ethA | 4328004 | c.-531C>T | upstream_gene_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4408029 | c.173delT | frameshift_variant | 1.0 |
