Run ID: SRR24256078
Sample name:
Date: 01-02-2024 15:37:22
Number of reads: 3721345
Percentage reads mapped: 99.5
Strain: lineage4.2.1.1
Drug-resistance: MDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Asp435Val (0.98) |
| Isoniazid | R | fabG1 c.-15C>T (0.97), katG p.Ser315Thr (1.00) |
| Ethambutol | R | embB p.Gly406Ser (1.00) |
| Pyrazinamide | R | pncA p.Val139Ala (0.98) |
| Streptomycin | R | rpsL p.Lys88Arg (0.99) |
| Fluoroquinolones | ||
| Moxifloxacin | ||
| Ofloxacin | ||
| Levofloxacin | ||
| Ciprofloxacin | ||
| Aminoglycosides | R | rrs n.1401A>G (1.00) |
| Amikacin | R | rrs n.1401A>G (1.00) |
| Capreomycin | R | rrs n.1401A>G (1.00) |
| Kanamycin | R | rrs n.1401A>G (1.00) |
| Cycloserine | ||
| Ethionamide | R | fabG1 c.-15C>T (0.97), ethA c.754_755dupGC (0.99), ethA c.754_755dupGC (0.99) |
| 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 | 0.99 |
| lineage4.2.1 | Euro-American (TUR) | H3;H4 | None | 0.99 |
| lineage4.2.1.1 | Euro-American (TUR) | H3;H4 | None | 0.99 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| rpoB | 761110 | p.Asp435Val | missense_variant | 0.98 | rifampicin |
| rpsL | 781822 | p.Lys88Arg | missense_variant | 0.99 | streptomycin |
| rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
| fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.97 | isoniazid, ethionamide |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| pncA | 2288826 | p.Val139Ala | missense_variant | 0.98 | pyrazinamide |
| embB | 4247729 | p.Gly406Ser | missense_variant | 1.0 | ethambutol |
| ethA | 4326718 | c.754_755dupGC | frameshift_variant | 0.99 | ethionamide, ethionamide |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
| mshA | 576108 | p.Ala254Gly | missense_variant | 0.33 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| mmpL5 | 776802 | p.Met560Thr | missense_variant | 0.99 |
| mmpL5 | 777451 | p.Val344Leu | missense_variant | 0.98 |
| 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 |
| PPE35 | 2169879 | p.Phe245Cys | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| Rv2752c | 3065958 | c.234G>A | synonymous_variant | 1.0 |
| ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.99 |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
| fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
| ddn | 3987092 | p.Glu83Asp | missense_variant | 1.0 |
| clpC1 | 4040786 | c.-82G>A | upstream_gene_variant | 0.98 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embA | 4243190 | c.-43G>C | upstream_gene_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4408213 | c.-11C>T | upstream_gene_variant | 0.99 |
