Run ID: ERR3335793
Sample name:
Date: 21-10-2023 15:23:25
Number of reads: 6658471
Percentage reads mapped: 99.41
Strain: lineage4.2.1
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.His445Asp (1.00) |
| Isoniazid | R | fabG1 c.-15C>T (0.99), katG p.Ser315Thr (1.00) |
| Ethambutol | R | embB p.Met306Ile (1.00) |
| Pyrazinamide | R | pncA c.-11A>G (1.00) |
| Streptomycin | R | gid p.Tyr22* (1.00) |
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | R | fabG1 c.-15C>T (0.99) |
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
| lineage4.2 | Euro-American | H;T;LAM | None | 1.0 |
| lineage4.2.1 | Euro-American (TUR) | H3;H4 | None | 0.99 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761139 | p.His445Asp | missense_variant | 1.0 | rifampicin |
| fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.99 | isoniazid, ethionamide |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| pncA | 2289252 | c.-11A>G | upstream_gene_variant | 1.0 | pyrazinamide |
| embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
| gid | 4408137 | p.Tyr22* | stop_gained | 1.0 | streptomycin |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 0.99 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rrl | 1473541 | n.-117G>T | upstream_gene_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| ndh | 2102247 | p.Val266Ile | missense_variant | 1.0 |
| PPE35 | 2168746 | p.Gly623Ser | missense_variant | 1.0 |
| PPE35 | 2169879 | p.Phe245Cys | missense_variant | 1.0 |
| Rv1979c | 2223284 | c.-120C>T | upstream_gene_variant | 0.99 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.99 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| Rv3236c | 3612746 | c.370delG | frameshift_variant | 0.99 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| aftB | 4267823 | c.1014G>C | synonymous_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4408149 | c.54T>C | synonymous_variant | 1.0 |
