Run ID: SRR8651588
Sample name:
Date: 21-10-2023 13:01:07
Number of reads: 10904720
Percentage reads mapped: 99.48
Strain: lineage4.4.2
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (1.00) |
| Isoniazid | R | katG p.Ser315Thr (1.00) |
| Ethambutol | R | embB p.Met306Val (1.00) |
| Pyrazinamide | ||
| Streptomycin | R | rpsL p.Lys88Arg (1.00) |
| Fluoroquinolones | R | gyrA p.Asp94Ala (0.99) |
| Moxifloxacin | R | gyrA p.Asp94Ala (0.99) |
| Ofloxacin | R | gyrA p.Asp94Ala (0.99) |
| Levofloxacin | R | gyrA p.Asp94Ala (0.99) |
| Ciprofloxacin | R | gyrA p.Asp94Ala (0.99) |
| 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 |
| lineage4.4 | Euro-American | S;T | None | 1.0 |
| lineage4.4.2 | Euro-American | T1;T2 | None | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Ala | missense_variant | 0.99 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
| rpsL | 781822 | p.Lys88Arg | missense_variant | 1.0 | streptomycin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| embB | 4247429 | p.Met306Val | missense_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 |
| mshA | 575886 | p.Leu180Arg | missense_variant | 0.99 |
| 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 | 2289102 | p.Thr47Ile | missense_variant | 1.0 |
| Rv2752c | 3066099 | p.Met31Ile | missense_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| Rv3083 | 3448348 | c.-156G>A | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embB | 4246508 | c.-6G>A | upstream_gene_variant | 1.0 |
| embB | 4247249 | p.Gly246Arg | missense_variant | 0.99 |
| aftB | 4267172 | p.Asp555Glu | missense_variant | 1.0 |
| aftB | 4268928 | c.-92C>T | upstream_gene_variant | 0.99 |
| aftB | 4269375 | c.-539G>A | upstream_gene_variant | 0.99 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
