Run ID: ERR4799641
Sample name:
Date: 20-10-2023 03:53:56
Number of reads: 4029808
Percentage reads mapped: 99.74
Strain: lineage4.8
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (0.99) |
| Isoniazid | R | fabG1 c.-15C>T (1.00), ahpC c.-48G>A (0.96) |
| Ethambutol | R | embB p.Met306Val (0.99) |
| Pyrazinamide | R | pncA p.Val128Gly (0.97) |
| Streptomycin | ||
| Fluoroquinolones | R | gyrA p.Ala90Val (0.98) |
| Moxifloxacin | R | gyrA p.Ala90Val (0.98) |
| Ofloxacin | R | gyrA p.Ala90Val (0.98) |
| Levofloxacin | R | gyrA p.Ala90Val (0.98) |
| Ciprofloxacin | R | gyrA p.Ala90Val (0.98) |
| 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 (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 | 0.99 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7570 | p.Ala90Val | missense_variant | 0.98 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin |
| rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
| fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
| pncA | 2288859 | p.Val128Gly | missense_variant | 0.97 | pyrazinamide |
| ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 0.96 | isoniazid |
| embB | 4247429 | p.Met306Val | missense_variant | 0.99 | ethambutol |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| rpoC | 766744 | p.Gln1125His | missense_variant | 0.98 |
| 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 | 0.95 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| katG | 2155229 | p.Gln295Lys | missense_variant | 0.95 |
| PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.98 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| folC | 2746198 | c.1401C>T | synonymous_variant | 0.99 |
| clpC1 | 4039729 | p.Asp326Asn | missense_variant | 0.99 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4408096 | p.Val36Ala | missense_variant | 0.99 |
| Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 0.97 |
