Run ID: SRR25207156
Sample name:
Date: 28-01-2024 11:01:00
Number of reads: 8314260
Percentage reads mapped: 99.49
Strain: lineage4.2.2
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (0.99) |
| Isoniazid | R | inhA p.Ser94Ala (0.99), katG p.Ser315Thr (0.99) |
| Ethambutol | R | embB p.Met306Ile (0.99), embB p.Gln497Lys (0.99) |
| Pyrazinamide | R | pncA c.317delT (0.99), pncA c.317delT (0.99) |
| Streptomycin | R | rpsL p.Lys43Arg (0.99) |
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | R | inhA p.Ser94Ala (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 | 0.99 |
| lineage4.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.99 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin |
| rpsL | 781687 | p.Lys43Arg | missense_variant | 0.99 | streptomycin |
| inhA | 1674481 | p.Ser94Ala | missense_variant | 0.99 | isoniazid, ethionamide |
| katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid |
| pncA | 2288924 | c.317delT | frameshift_variant | 0.99 | pyrazinamide, pyrazinamide |
| embB | 4247431 | p.Met306Ile | missense_variant | 0.99 | ethambutol |
| embB | 4248002 | p.Gln497Lys | missense_variant | 0.99 | 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 |
| gyrA | 9368 | c.2067G>A | synonymous_variant | 0.99 |
| mshA | 576077 | c.730C>T | synonymous_variant | 1.0 |
| rpoC | 766625 | c.3256C>T | synonymous_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 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2289168 | p.Ala25Val | missense_variant | 1.0 |
| Rv2752c | 3066280 | c.-89C>T | 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 |
| fbiD | 3339211 | p.Ala32Thr | missense_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| Rv3236c | 3612469 | c.648A>G | synonymous_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| ethA | 4327443 | p.Gly11Ser | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
