Run ID: ERR10610349
Sample name:
Date: 23-05-2023 01:07:13
Number of reads: 3627295
Percentage reads mapped: 99.29
Strain: lineage4.1.1
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.His445Asp (1.00) |
| Isoniazid | R | katG p.Ser315Thr (0.99) |
| Ethambutol | R | embB p.Met306Val (0.98) |
| Pyrazinamide | R | pncA p.Gly97Cys (0.99) |
| Streptomycin | R | gid c.351delG (1.00) |
| Fluoroquinolones | R | gyrA p.Asp94Asn (0.98) |
| Moxifloxacin | R | gyrA p.Asp94Asn (0.98) |
| Ofloxacin | R | gyrA p.Asp94Asn (0.98) |
| Levofloxacin | R | gyrA p.Asp94Asn (0.98) |
| Ciprofloxacin | R | gyrA p.Asp94Asn (0.98) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | R | ethA c.851delC (0.98), ethA c.851delC (0.98) |
| 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 | 0.99 |
| lineage4.1.1 | Euro-American (X-type) | X1;X2;X3 | None | 0.99 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7581 | p.Asp94Asn | missense_variant | 0.98 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761139 | p.His445Asp | missense_variant | 1.0 | rifampicin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid |
| pncA | 2288953 | p.Gly97Cys | missense_variant | 0.99 | pyrazinamide |
| embB | 4247429 | p.Met306Val | missense_variant | 0.98 | ethambutol |
| ethA | 4326622 | c.851delC | frameshift_variant | 0.98 | ethionamide, ethionamide |
| gid | 4407851 | c.351delG | frameshift_variant | 1.0 | streptomycin |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 0.98 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 0.99 |
| rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.99 |
| 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 |
| ahpC | 2726210 | c.18T>C | synonymous_variant | 0.98 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| Rv3083 | 3449840 | p.Arg446His | missense_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 0.99 |
| fbiA | 3641447 | p.Thr302Met | missense_variant | 1.0 |
| rpoA | 3877553 | p.Glu319Lys | missense_variant | 0.98 |
| embC | 4240897 | c.1035C>G | synonymous_variant | 0.99 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embC | 4242803 | p.Val981Leu | missense_variant | 0.99 |
| embB | 4249408 | c.2895G>A | synonymous_variant | 0.99 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
