Run ID: ERR4798135
Sample name:
Date: 20-10-2023 02:45:14
Number of reads: 5125719
Percentage reads mapped: 99.57
Strain: lineage4.2.2.2
Drug-resistance: XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (1.00) |
| Isoniazid | R | katG p.Ser315Thr (1.00), katG p.Thr275Ala (1.00) |
| Ethambutol | R | embB p.Met306Ile (1.00) |
| Pyrazinamide | ||
| Streptomycin | R | rpsL p.Lys43Arg (1.00), gid c.102delG (1.00) |
| 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 | R | tlyA c.273_274delAT (1.00), tlyA c.273_274delAT (1.00) |
| Kanamycin | ||
| Cycloserine | R | ald c.464delG (0.50) |
| Ethionamide | R | ethA p.Thr88Ile (1.00) |
| Clofazimine | ||
| Para-aminosalicylic_acid | ||
| Delamanid | ||
| Bedaquiline | ||
| Linezolid | R | rrl n.2814G>T (1.00) |
| 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 | 1.0 |
| lineage4.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.83 |
| lineage4.2.2.2 | Euro-American (Ural) | T;LAM7-TUR | None | 0.99 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7582 | p.Asp94Gly | missense_variant | 0.99 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
| rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
| rrl | 1476471 | n.2814G>T | non_coding_transcript_exon_variant | 1.0 | linezolid |
| tlyA | 1918211 | c.273_274delAT | frameshift_variant | 1.0 | capreomycin, capreomycin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| katG | 2155289 | p.Thr275Ala | missense_variant | 1.0 | isoniazid |
| ald | 3087278 | c.464delG | frameshift_variant | 0.5 | cycloserine |
| embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
| ethA | 4327211 | p.Thr88Ile | missense_variant | 1.0 | ethionamide |
| gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 5965 | c.726A>G | synonymous_variant | 1.0 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 8688 | p.Ala463Ser | missense_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| gyrA | 9328 | p.Ala676Val | missense_variant | 1.0 |
| mshA | 576077 | c.730C>T | synonymous_variant | 1.0 |
| rpoB | 761489 | c.1683G>A | synonymous_variant | 1.0 |
| rpoC | 766485 | p.Val1039Gly | missense_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
| fbiC | 1305180 | c.2250G>A | synonymous_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rrl | 1475927 | n.2270G>T | non_coding_transcript_exon_variant | 0.69 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| PPE35 | 2167937 | c.2676A>G | synonymous_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 1.0 |
| ald | 3086742 | c.-78A>C | upstream_gene_variant | 1.0 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| ald | 3087807 | c.991dupG | frameshift_variant | 0.86 |
| Rv3083 | 3449705 | p.Ile401Thr | missense_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| whiB6 | 4338513 | c.9C>T | synonymous_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
