Run ID: ERR1193842
Sample name:
Date: 19-10-2023 17:32:15
Number of reads: 1821542
Percentage reads mapped: 97.97
Strain: lineage4.3
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (1.00) |
| Isoniazid | R | fabG1 c.-15C>T (1.00) |
| Ethambutol | R | embB p.Met306Val (1.00) |
| Pyrazinamide | R | pncA p.Ser66Pro (1.00) |
| Streptomycin | ||
| Fluoroquinolones | R | gyrA p.Asp94Tyr (1.00) |
| Moxifloxacin | R | gyrA p.Asp94Tyr (1.00) |
| Ofloxacin | R | gyrA p.Asp94Tyr (1.00) |
| Levofloxacin | R | gyrA p.Asp94Tyr (1.00) |
| Ciprofloxacin | R | gyrA p.Asp94Tyr (1.00) |
| Aminoglycosides | R | rrs n.1401A>G (0.99) |
| Amikacin | R | rrs n.1401A>G (0.99) |
| Capreomycin | R | rrs n.1401A>G (0.99) |
| Kanamycin | R | rrs n.1401A>G (0.99) |
| Cycloserine | ||
| Ethionamide | R | fabG1 c.-15C>T (1.00), ethA c.774delG (1.00), ethA c.774delG (1.00) |
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid |
| Lineage | Family | Main Spoligotype | RDs | Frequency |
|---|---|---|---|---|
| lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
| lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7581 | p.Asp94Tyr | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
| rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.99 | kanamycin, capreomycin, aminoglycosides, amikacin |
| fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
| pncA | 2289046 | p.Ser66Pro | missense_variant | 1.0 | pyrazinamide |
| embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
| ethA | 4326699 | c.774delG | frameshift_variant | 1.0 | ethionamide, ethionamide |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7580 | c.279C>T | synonymous_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| rpoC | 764995 | c.1626C>G | 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 |
| ndh | 2102709 | p.Tyr112Asp | missense_variant | 0.99 |
| katG | 2154240 | p.Met624Ile | missense_variant | 1.0 |
| katG | 2154710 | p.Thr468Pro | missense_variant | 1.0 |
| katG | 2156138 | c.-27A>G | upstream_gene_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| eis | 2715555 | c.-223G>A | upstream_gene_variant | 1.0 |
| thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.99 |
| embC | 4240172 | p.Val104Met | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| aftB | 4268096 | c.741C>A | synonymous_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407807 | p.Asp132Glu | missense_variant | 1.0 |
| gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |
