Run ID: SRR6824366
Sample name:
Date: 20-10-2023 19:46:40
Number of reads: 5790702
Percentage reads mapped: 93.97
Strain: lineage4.5
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.His445Asp (1.00) |
| Isoniazid | ||
| Ethambutol | R | embB p.Met306Val (1.00) |
| Pyrazinamide | R | pncA p.Gln10Arg (1.00) |
| Streptomycin | ||
| Fluoroquinolones | R | gyrB p.Arg446His (0.98) |
| Moxifloxacin | R | gyrB p.Arg446His (0.98) |
| Ofloxacin | R | gyrB p.Arg446His (0.98) |
| Levofloxacin | R | gyrB p.Arg446His (0.98) |
| Ciprofloxacin | R | gyrB p.Arg446His (0.98) |
| 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 |
|---|---|---|---|---|---|
| gyrB | 6576 | p.Arg446His | missense_variant | 0.98 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761139 | p.His445Asp | missense_variant | 1.0 | rifampicin |
| pncA | 2289213 | p.Gln10Arg | missense_variant | 1.0 | pyrazinamide |
| embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 5359 | c.120C>T | synonymous_variant | 0.99 |
| gyrB | 5430 | p.Thr64Ile | missense_variant | 1.0 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 7892 | c.591G>A | synonymous_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| fgd1 | 491625 | c.843C>G | synonymous_variant | 1.0 |
| ccsA | 620029 | c.139C>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 |
| katG | 2154661 | p.Arg484His | missense_variant | 1.0 |
| PPE35 | 2170568 | p.Ile15Met | missense_variant | 0.99 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2290077 | c.-836G>T | upstream_gene_variant | 1.0 |
| ahpC | 2726146 | c.-47_-46insT | upstream_gene_variant | 1.0 |
| Rv3083 | 3448560 | c.57G>A | synonymous_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 0.97 |
| clpC1 | 4038318 | p.Pro796Leu | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
