Run ID: ERR4813950
Sample name:
Date: 20-10-2023 14:49:20
Number of reads: 3072456
Percentage reads mapped: 99.73
Strain: lineage4.8
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (1.00) |
| Isoniazid | R | fabG1 c.-15C>T (0.99), inhA p.Ile21Thr (1.00) |
| Ethambutol | R | embB p.Met306Ile (1.00) |
| Pyrazinamide | R | pncA c.407_408insG (1.00) |
| Streptomycin | R | rrs n.517C>T (1.00) |
| Fluoroquinolones | R | gyrB p.Glu501Asp (1.00) |
| Moxifloxacin | R | gyrB p.Glu501Asp (1.00) |
| Ofloxacin | R | gyrB p.Glu501Asp (1.00) |
| Levofloxacin | R | gyrB p.Glu501Asp (1.00) |
| Ciprofloxacin | R | gyrB p.Glu501Asp (1.00) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | R | fabG1 c.-15C>T (0.99), inhA p.Ile21Thr (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 | 1.0 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrB | 6742 | p.Glu501Asp | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
| rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 1.0 | streptomycin |
| fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 0.99 | isoniazid, ethionamide |
| inhA | 1674263 | p.Ile21Thr | missense_variant | 1.0 | isoniazid, ethionamide |
| pncA | 2288834 | c.407_408insG | frameshift_variant | 1.0 | pyrazinamide |
| embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.99 |
| rplC | 800906 | p.Pro33Leu | missense_variant | 1.0 |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
| rrs | 1471781 | n.-65G>A | upstream_gene_variant | 0.99 |
| rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.99 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| thyA | 3073768 | p.Arg235Leu | missense_variant | 1.0 |
| alr | 3840764 | c.657G>C | synonymous_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| aftB | 4268837 | c.-1C>G | upstream_gene_variant | 1.0 |
| ubiA | 4269296 | p.Met180Val | missense_variant | 0.99 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4407940 | p.Val88Gly | missense_variant | 1.0 |
| Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |
