Run ID: ERR6197035
Sample name:
Date: 2024-04-14T10:12:33.792111
Number of reads: 1745073
Percentage reads mapped: 95.33
Median coverage: 53.0
Strain: lineage4.7
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.7 | Euro-American (mainly T) | None | 0.99 |
| lineage4 | Euro-American | None | 1.0 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| dnaA | 1126 | c.1126C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.1 | rifampicin | |
| rpoB | 763005 | c.3199_3201delTGCinsGG | frameshift_variant&missense_variant | 0.11 | rifampicin | |
| rpoC | 763468 | c.99G>C | synonymous_variant | 0.11 | rifampicin | Not assoc w R - Interim |
| rpoC | 763483 | c.114G>C | synonymous_variant | 0.11 | rifampicin | |
| rpoC | 763534 | c.165T>C | synonymous_variant | 0.1 | rifampicin | |
| rpoC | 763546 | c.177A>G | synonymous_variant | 0.11 | rifampicin | Not assoc w R - Interim |
| rpoC | 763550 | p.Tyr61Ala | missense_variant | 0.11 | rifampicin | |
| rpoC | 763570 | c.201G>C | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
| rpoC | 763573 | c.204G>T | synonymous_variant | 0.11 | rifampicin | |
| rpoC | 763578 | p.Phe70Tyr | missense_variant | 0.13 | rifampicin | |
| rpoC | 763594 | c.225C>T | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rpsL | 781443 | c.-117T>G | upstream_gene_variant | 1.0 | streptomycin | |
| Rv1258c | 1407604 | c.-264C>T | upstream_gene_variant | 1.0 | streptomycin | |
| isoniazid | ||||||
| pyrazinamide | ||||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 0.91 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476298 | n.2641C>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476300 | n.2643G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476301 | n.2644A>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476307 | n.2650A>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476309 | n.2652G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rpsA | 1834294 | c.753G>C | synonymous_variant | 0.1 | pyrazinamide | |
| rpsA | 1834298 | p.Gln253Glu | missense_variant | 0.1 | pyrazinamide | |
| rpsA | 1834306 | c.765T>C | synonymous_variant | 0.14 | pyrazinamide | |
| rpsA | 1834312 | c.771G>A | synonymous_variant | 0.12 | pyrazinamide | |
| rpsA | 1834327 | c.786G>T | synonymous_variant | 0.12 | pyrazinamide | |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| PPE35 | 2170675 | c.-63G>C | upstream_gene_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| pepQ | 2859961 | p.Ala153Gly | missense_variant | 1.0 | clofazimine | Uncertain significance |
| bedaquiline | Uncertain significance | |||||
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4249732 | c.3219C>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R |
