Run ID: ERR4798983
Sample name:
Date: 20-10-2023 03:16:41
Number of reads: 8050245
Percentage reads mapped: 99.5
Strain: lineage4.2.2.2
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (1.00) |
| Isoniazid | R | katG p.Ser315Thr (0.99) |
| Ethambutol | R | embB p.Gly406Cys (0.99) |
| Pyrazinamide | R | pncA p.Val139Gly (0.99) |
| Streptomycin | R | rpsL p.Lys88Met (0.98) |
| Fluoroquinolones | R | gyrA p.Ala90Val (0.99) |
| Moxifloxacin | R | gyrA p.Ala90Val (0.99) |
| Ofloxacin | R | gyrA p.Ala90Val (0.99) |
| Levofloxacin | R | gyrA p.Ala90Val (0.99) |
| Ciprofloxacin | R | gyrA p.Ala90Val (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 |
| lineage4.2 | Euro-American | H;T;LAM | None | 0.98 |
| lineage4.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.98 |
| lineage4.2.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.99 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7570 | p.Ala90Val | missense_variant | 0.99 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
| rpsL | 781822 | p.Lys88Met | missense_variant | 0.98 | streptomycin |
| katG | 2155167 | p.Ser315Thr | missense_variant | 0.99 | isoniazid |
| pncA | 2288826 | p.Val139Gly | missense_variant | 0.99 | pyrazinamide |
| embB | 4247729 | p.Gly406Cys | missense_variant | 0.99 | 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 | 8688 | p.Ala463Ser | missense_variant | 0.99 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| mshA | 576077 | c.730C>T | synonymous_variant | 0.97 |
| rpoB | 761489 | c.1683G>A | synonymous_variant | 0.97 |
| rpoC | 764817 | p.Val483Gly | missense_variant | 0.98 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776402 | c.2079C>G | synonymous_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 |
| ribD | 2986827 | c.-12G>A | upstream_gene_variant | 0.98 |
| Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 0.99 |
| ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.96 |
| 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 |
| embB | 4248004 | p.Gln497His | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
