Run ID: ERR4800294
Sample name:
Date: 20-10-2023 04:15:51
Number of reads: 2770066
Percentage reads mapped: 99.7
Strain: lineage4.3.3
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Thr427Pro (0.97), rpoB p.Ser450Trp (1.00) |
| Isoniazid | R | katG p.Ser315Thr (0.97) |
| Ethambutol | R | embB p.Met306Val (1.00) |
| Pyrazinamide | R | pncA p.Ser67Pro (0.99) |
| Streptomycin | R | gid p.Pro75Arg (0.96) |
| Fluoroquinolones | R | gyrA p.Asp94Gly (0.99) |
| Moxifloxacin | R | gyrA p.Asp94Gly (0.99) |
| Ofloxacin | R | gyrA p.Asp94Gly (0.99) |
| Levofloxacin | R | gyrA p.Asp94Gly (0.99) |
| Ciprofloxacin | R | gyrA p.Asp94Gly (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 |
| lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 0.98 |
| lineage4.3.3 | Euro-American (LAM) | LAM;T | RD115 | 0.98 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Gly | missense_variant | 0.99 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761085 | p.Thr427Pro | missense_variant | 0.97 | rifampicin |
| rpoB | 761155 | p.Ser450Trp | missense_variant | 1.0 | rifampicin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 0.97 | isoniazid |
| pncA | 2289043 | p.Ser67Pro | missense_variant | 0.99 | pyrazinamide |
| embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
| gid | 4407979 | p.Pro75Arg | missense_variant | 0.96 | streptomycin |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 8040 | p.Gly247Ser | missense_variant | 0.99 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| gyrA | 9407 | c.2106C>T | synonymous_variant | 1.0 |
| rpoC | 764995 | c.1626C>G | synonymous_variant | 0.99 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| Rv1258c | 1407363 | c.-23C>T | upstream_gene_variant | 0.97 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rpsA | 1834836 | p.Met432Thr | missense_variant | 0.93 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| katG | 2156196 | c.-85C>T | upstream_gene_variant | 0.97 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| kasA | 2518919 | p.Gly269Ser | missense_variant | 1.0 |
| folC | 2746340 | p.Ala420Val | missense_variant | 1.0 |
| thyX | 3067954 | c.-9G>A | upstream_gene_variant | 0.99 |
| thyA | 3073868 | p.Thr202Ala | missense_variant | 0.98 |
| thyA | 3074096 | p.Arg126Gly | missense_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| rpoA | 3877954 | p.Gln185Arg | missense_variant | 0.98 |
| clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.96 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| ethA | 4327296 | p.Tyr60Asp | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| whiB6 | 4338599 | c.-78A>G | upstream_gene_variant | 0.26 |
| gid | 4408156 | p.Leu16Arg | missense_variant | 0.99 |
