Run ID: SRR6397917
Sample name:
Date: 2024-10-05T02:29:00.476279
Number of reads: 4168465
Percentage reads mapped: 94.62
Median coverage: 118.0
Strain: lineage4.5
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.5 | Euro-American | RD122 | 1.0 |
| 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 |
|---|---|---|---|---|---|---|
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7892 | c.591G>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| ccsA | 620029 | c.139C>T | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
| capreomycin | Not assoc w R - Interim | |||||
| amikacin | Not assoc w R - Interim | |||||
| hadA | 731875 | c.-55G>A | upstream_gene_variant | 0.99 | isoniazid | |
| rpoC | 766883 | p.Ser1172Ala | missense_variant | 0.98 | rifampicin | Uncertain significance |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476368 | n.2711T>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.18 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.18 | capreomycin | |
| linezolid | ||||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.21 | capreomycin | |
| linezolid | ||||||
| rrl | 1476428 | n.2771C>A | non_coding_transcript_exon_variant | 0.24 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
| linezolid | ||||||
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.12 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 0.99 | capreomycin | Not assoc w R |
| bacA | 2062992 | c.1737G>C | synonymous_variant | 0.99 | kanamycin | |
| capreomycin | ||||||
| streptomycin | Not assoc w R - Interim | |||||
| amikacin | ||||||
| katG | 2156611 | c.-500G>T | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
| PPE35 | 2170568 | p.Ile15Met | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| folC | 2747723 | c.-125G>A | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| Rv3083 | 3449940 | c.1437T>C | synonymous_variant | 1.0 | ethionamide | |
| lpqB | 3623176 | p.Pro579Ala | missense_variant | 1.0 | rifampicin | Uncertain significance |
| bedaquiline | ||||||
| lpqB | 3623462 | c.1449G>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| bedaquiline | ||||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
| clpC1 | 4038318 | p.Pro796Leu | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| embC | 4240817 | p.Thr319Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embC | 4242643 | c.2781C>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R |
| aftB | 4268495 | c.342G>C | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| whiB6 | 4338926 | c.-405T>C | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin |
