Run ID: ERR11488412
Sample name:
Date: 08-01-2024 11:04:20
Number of reads: 5658032
Percentage reads mapped: 99.65
Strain: lineage4.8
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Trp (1.00) |
| Isoniazid | R | katG p.Ser315Thr (1.00) |
| Ethambutol | R | embB p.Met306Ile (1.00) |
| Pyrazinamide | R | pncA p.Val7Gly (1.00) |
| Streptomycin | R | gid c.351delG (0.99) |
| Fluoroquinolones | R | gyrB p.Arg446His (1.00) |
| Moxifloxacin | R | gyrB p.Arg446His (1.00) |
| Ofloxacin | R | gyrB p.Arg446His (1.00) |
| Levofloxacin | R | gyrB p.Arg446His (1.00) |
| Ciprofloxacin | R | gyrB p.Arg446His (1.00) |
| 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 | ethA c.341delA (0.99), ethA c.341delA (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 |
| lineage4.8 | Euro-American (mainly T) | T1;T2;T3;T5 | RD219 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrB | 6576 | p.Arg446His | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Trp | missense_variant | 1.0 | rifampicin |
| rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| pncA | 2289222 | p.Val7Gly | missense_variant | 1.0 | pyrazinamide |
| embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
| ethA | 4327132 | c.341delA | frameshift_variant | 0.99 | ethionamide, ethionamide |
| gid | 4407851 | c.351delG | frameshift_variant | 0.99 | streptomycin |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrB | 6455 | p.Val406Ile | missense_variant | 1.0 |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| gyrA | 8676 | p.Glu459Gln | missense_variant | 1.0 |
| rpoB | 761060 | c.1254C>T | synonymous_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.99 |
| fbiC | 1303157 | p.His76Pro | missense_variant | 0.28 |
| 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 |
| PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| clpC1 | 4039729 | p.Asp326Asn | missense_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.99 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
