Run ID: ERR8975781
Sample name:
Date: 20-10-2023 15:46:02
Number of reads: 6445518
Percentage reads mapped: 99.58
Strain: lineage4.1.1.3
Drug-resistance: XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (1.00) |
| Isoniazid | R | katG p.Ser315Thr (1.00), ahpC c.-48G>A (1.00) |
| Ethambutol | R | embB p.Asp328Tyr (1.00), embB p.Asp1024Asn (1.00) |
| Pyrazinamide | R | pncA p.Val180Ala (1.00), pncA c.470delT (0.74) |
| Streptomycin | R | rpsL p.Lys43Arg (1.00) |
| Fluoroquinolones | R | gyrA p.Asp94Gly (1.00) |
| Moxifloxacin | R | gyrA p.Asp94Gly (1.00) |
| Ofloxacin | R | gyrA p.Asp94Gly (1.00) |
| Levofloxacin | R | gyrA p.Asp94Gly (1.00) |
| Ciprofloxacin | R | gyrA p.Asp94Gly (1.00) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | R | eis c.-10G>A (1.00) |
| Cycloserine | ||
| Ethionamide | R | ethA c.597delC (1.00), ethA c.597delC (1.00) |
| Clofazimine | R | mmpR5 c.198dupG (0.13) |
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | R | mmpR5 c.198dupG (0.13) |
| 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 |
| lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 1.0 |
| lineage4.1.1.3 | Euro-American (X-type) | X1;X3 | RD193 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
| mmpR5 | 779181 | c.198dupG | frameshift_variant | 0.13 | clofazimine, bedaquiline |
| rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
| katG | 2155167 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| pncA | 2288703 | p.Val180Ala | missense_variant | 1.0 | pyrazinamide |
| pncA | 2288771 | c.470delT | frameshift_variant | 0.74 | pyrazinamide |
| eis | 2715342 | c.-10G>A | upstream_gene_variant | 1.0 | kanamycin |
| ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 1.0 | isoniazid |
| embB | 4247495 | p.Asp328Tyr | missense_variant | 1.0 | ethambutol |
| embB | 4249583 | p.Asp1024Asn | missense_variant | 1.0 | ethambutol |
| ethA | 4326876 | c.597delC | frameshift_variant | 1.0 | ethionamide, ethionamide |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 6608 | p.Val457Leu | missense_variant | 1.0 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpR5 | 779130 | c.144dupC | frameshift_variant | 0.85 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| rplC | 801354 | c.546G>A | synonymous_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 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| Rv3083 | 3449616 | p.Met371Ile | missense_variant | 1.0 |
| 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 |
| embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 |
| whiB6 | 4338286 | p.Val79Gly | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
