Run ID: SRR6824337
Sample name:
Date: 20-10-2023 19:42:15
Number of reads: 18464360
Percentage reads mapped: 99.06
Strain: lineage4.5
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Tyr (1.00) |
| Isoniazid | R | katG p.Ala172Val (1.00), ahpC c.-48G>A (1.00) |
| Ethambutol | R | embA c.-16C>T (1.00) |
| Pyrazinamide | ||
| Streptomycin | R | rrs n.514A>C (0.99) |
| Fluoroquinolones | R | gyrA p.Ala90Val (1.00) |
| Moxifloxacin | R | gyrA p.Ala90Val (1.00) |
| Ofloxacin | R | gyrA p.Ala90Val (1.00) |
| Levofloxacin | R | gyrA p.Ala90Val (1.00) |
| Ciprofloxacin | R | gyrA p.Ala90Val (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 |
| lineage4.5 | Euro-American | H;T | RD122 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Tyr | missense_variant | 1.0 | rifampicin |
| rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 0.99 | streptomycin |
| katG | 2155597 | p.Ala172Val | missense_variant | 1.0 | isoniazid |
| ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 1.0 | isoniazid |
| embA | 4243217 | c.-16C>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 | 7892 | c.591G>A | synonymous_variant | 0.99 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| ccsA | 620029 | c.139C>T | synonymous_variant | 0.99 |
| rpoB | 759636 | c.-171C>T | upstream_gene_variant | 0.99 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 777810 | p.Arg224Gln | 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 |
| PPE35 | 2170568 | p.Ile15Met | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2289082 | p.Pro54Ser | missense_variant | 1.0 |
| eis | 2715536 | c.-204C>T | upstream_gene_variant | 0.99 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| Rv3236c | 3612102 | p.Ile339Val | missense_variant | 1.0 |
| rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 1.0 |
| clpC1 | 4038318 | p.Pro796Leu | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4243156 | c.-77T>G | upstream_gene_variant | 1.0 |
| embB | 4247595 | p.Cys361Tyr | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| whiB6 | 4338599 | c.-78A>C | upstream_gene_variant | 0.99 |
| gid | 4407587 | p.Arg206Gly | missense_variant | 1.0 |
