Run ID: ERR1213904
Sample name:
Date: 19-10-2023 21:32:47
Number of reads: 5557844
Percentage reads mapped: 98.87
Strain: lineage4.1.2.1
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Val170Phe (0.99) |
| Isoniazid | R | fabG1 c.-15C>T (1.00), inhA p.Ser94Ala (1.00) |
| Ethambutol | R | embB p.Asp1024Asn (1.00) |
| Pyrazinamide | R | pncA p.Thr76Pro (1.00) |
| Streptomycin | ||
| Fluoroquinolones | R | gyrB p.Asn499Asp (0.99) |
| Moxifloxacin | R | gyrB p.Asn499Asp (0.99) |
| Ofloxacin | R | gyrB p.Asn499Asp (0.99) |
| Levofloxacin | R | gyrB p.Asn499Asp (0.99) |
| Ciprofloxacin | R | gyrB p.Asn499Asp (0.99) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | R | fabG1 c.-15C>T (1.00), inhA p.Ser94Ala (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 |
| lineage4.1 | Euro-American | T;X;H | None | 1.0 |
| lineage4.1.2 | Euro-American | T;H | None | 1.0 |
| lineage4.1.2.1 | Euro-American (Haarlem) | T1;H1 | RD182 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrB | 6734 | p.Asn499Asp | missense_variant | 0.99 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 760314 | p.Val170Phe | missense_variant | 0.99 | rifampicin |
| fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
| inhA | 1674481 | p.Ser94Ala | missense_variant | 1.0 | isoniazid, ethionamide |
| pncA | 2289016 | p.Thr76Pro | missense_variant | 1.0 | pyrazinamide |
| embB | 4249583 | p.Asp1024Asn | 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 |
| fgd1 | 491591 | p.Lys270Met | missense_variant | 0.98 |
| mshA | 575679 | p.Asn111Ser | missense_variant | 1.0 |
| rpoB | 760115 | c.309C>T | synonymous_variant | 1.0 |
| rpoB | 762201 | p.Lys799Gln | missense_variant | 0.95 |
| rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpR5 | 779116 | c.130_139delCTGGTGTGTG | frameshift_variant | 0.97 |
| 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 |
| kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.99 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embC | 4242803 | p.Val981Leu | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407790 | p.Ala138Val | missense_variant | 1.0 |
