Run ID: ERR2516502
Sample name:
Date: 19-10-2023 23:45:58
Number of reads: 8336923
Percentage reads mapped: 99.76
Strain: lineage4.8
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Trp (1.00) |
| Isoniazid | R | fabG1 c.-17G>T (1.00), inhA p.Ser94Ala (1.00), katG p.Phe567Ser (1.00) |
| Ethambutol | R | embA c.-12C>T (0.34), embB p.Met306Ile (0.64), embB p.Gly406Asp (1.00) |
| Pyrazinamide | R | pncA p.Asp63Ala (0.35), pncA p.Ile31Ser (0.73) |
| Streptomycin | R | gid c.102delG (1.00) |
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | R | fabG1 c.-17G>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 |
| lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761155 | p.Ser450Trp | missense_variant | 1.0 | rifampicin |
| fabG1 | 1673423 | c.-17G>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
| inhA | 1674481 | p.Ser94Ala | missense_variant | 1.0 | isoniazid, ethionamide |
| katG | 2154412 | p.Phe567Ser | missense_variant | 1.0 | isoniazid |
| pncA | 2289054 | p.Asp63Ala | missense_variant | 0.35 | pyrazinamide |
| pncA | 2289150 | p.Ile31Ser | missense_variant | 0.73 | pyrazinamide |
| embA | 4243221 | c.-12C>T | upstream_gene_variant | 0.34 | ethambutol |
| embB | 4247431 | p.Met306Ile | missense_variant | 0.64 | ethambutol |
| embB | 4247730 | p.Gly406Asp | missense_variant | 1.0 | ethambutol |
| gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| ccsA | 620475 | c.585G>A | synonymous_variant | 1.0 |
| rpoB | 762391 | p.Leu862Arg | missense_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 |
| rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| tlyA | 1918745 | c.806A>G | stop_lost&splice_region_variant | 0.99 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2289656 | c.-415C>A | upstream_gene_variant | 1.0 |
| folC | 2747612 | c.-14T>G | upstream_gene_variant | 1.0 |
| ald | 3087095 | c.276C>T | synonymous_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embB | 4245899 | c.-615C>T | upstream_gene_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| whiB6 | 4338632 | c.-112_-111insTTAACAGG | upstream_gene_variant | 1.0 |
| Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |
