Run ID: ERR4799172
Sample name:
Date: 20-10-2023 03:44:27
Number of reads: 3168331
Percentage reads mapped: 99.68
Strain: lineage4.8
Drug-resistance: Pre-XDR-TB
| Drug | Resistance | Supporting mutations |
|---|---|---|
| Rifampicin | R | rpoB p.Ser450Leu (1.00) |
| Isoniazid | R | katG p.Ser315Thr (1.00) |
| Ethambutol | R | embB p.His1002Arg (0.96) |
| Pyrazinamide | R | pncA c.391dupG (0.98), pncA c.391dupG (0.98) |
| Streptomycin | ||
| Fluoroquinolones | R | gyrA p.Asp94His (0.99) |
| Moxifloxacin | R | gyrA p.Asp94His (0.99) |
| Ofloxacin | R | gyrA p.Asp94His (0.99) |
| Levofloxacin | R | gyrA p.Asp94His (0.99) |
| Ciprofloxacin | R | gyrA p.Asp94His (0.99) |
| Aminoglycosides | ||
| Amikacin | ||
| Capreomycin | ||
| Kanamycin | ||
| Cycloserine | ||
| Ethionamide | R | ethA c.655dupG (0.12), ethA c.550_551dupGG (0.80) |
| 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 | 0.98 |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
|---|---|---|---|---|---|
| gyrA | 7581 | p.Asp94His | missense_variant | 0.99 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
| rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
| katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
| pncA | 2288850 | c.391dupG | frameshift_variant | 0.98 | pyrazinamide, pyrazinamide |
| embB | 4249518 | p.His1002Arg | missense_variant | 0.96 | ethambutol |
| ethA | 4326818 | c.655dupG | frameshift_variant | 0.12 | ethionamide |
| ethA | 4326922 | c.550_551dupGG | frameshift_variant | 0.8 | ethionamide |
| Gene | Chromosome position | Mutation | Type | Estimated fraction |
|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
| rpoC | 764669 | p.Pro434Thr | missense_variant | 0.85 |
| rpoC | 764817 | p.Val483Ala | missense_variant | 0.1 |
| 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 |
| rrs | 1472753 | n.908A>C | non_coding_transcript_exon_variant | 0.98 |
| rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
| pncA | 2289969 | c.-728G>C | upstream_gene_variant | 1.0 |
| ald | 3087647 | c.830dupG | frameshift_variant | 1.0 |
| embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
| embB | 4247028 | p.Leu172Arg | missense_variant | 0.17 |
| ubiA | 4269124 | p.Ala237Val | missense_variant | 0.97 |
| ethR | 4326844 | c.-705G>C | upstream_gene_variant | 0.99 |
| whiB6 | 4338362 | p.Arg54Gly | missense_variant | 1.0 |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
| gid | 4408061 | p.His48Asn | missense_variant | 0.99 |
| Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 0.98 |
