Run ID: SRR26159035
Sample name:
Date: 2024-10-05T06:45:34.803661
Number of reads: 68058
Percentage reads mapped: 99.47
Median coverage: 0.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.9 | Euro-American (H37Rv-like) | 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 | 7607 | c.306C>G | synonymous_variant | 0.99 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 7628 | c.327G>C | synonymous_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7631 | c.330G>C | synonymous_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7637 | c.336C>G | synonymous_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7658 | c.357A>G | synonymous_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7661 | c.360C>T | synonymous_variant | 0.98 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7664 | c.363T>C | synonymous_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7670 | c.369A>G | synonymous_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7676 | c.375G>C | synonymous_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7679 | c.378G>C | synonymous_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7697 | c.396C>G | synonymous_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7700 | c.399G>C | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7706 | c.405C>G | synonymous_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7710 | c.409T>C | synonymous_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7721 | c.420G>A | synonymous_variant | 0.99 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| gyrA | 7725 | c.424C>T | synonymous_variant | 0.99 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | ||||||
| gyrA | 7728 | c.427_429delAGGinsCGT | synonymous_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7739 | c.438C>T | synonymous_variant | 0.99 | levofloxacin | |
| moxifloxacin | Not assoc w R - Interim | |||||
| rrs | 1472169 | n.324A>G | non_coding_transcript_exon_variant | 0.45 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472251 | n.406G>A | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Not assoc w R | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1472286 | n.441C>A | non_coding_transcript_exon_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1473104 | n.1259C>T | non_coding_transcript_exon_variant | 0.99 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473110 | n.1265T>G | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473111 | n.1266A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473123 | n.1278delAinsTT | non_coding_transcript_exon_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1475991 | n.2334T>C | non_coding_transcript_exon_variant | 0.98 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1475995 | n.2338G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476030 | n.2373A>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476032 | n.2375C>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476033 | n.2376T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476034 | n.2377C>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476044 | n.2387T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476045 | n.2388G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476047 | n.2390G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476049 | n.2392C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476077 | n.2420T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476088 | n.2431A>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476103 | n.2446C>G | non_coding_transcript_exon_variant | 0.93 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476105 | n.2448_2449delGAinsCT | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476110 | n.2453G>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476115 | n.2458T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476119 | n.2462G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476131 | n.2474C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476214 | n.2557G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476215 | n.2558C>T | non_coding_transcript_exon_variant | 0.87 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.83 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476251 | n.2594T>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476252 | n.2595T>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476256 | n.2599A>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 0.83 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476393 | n.2736C>T | non_coding_transcript_exon_variant | 0.46 | capreomycin | |
| linezolid | ||||||
| rrl | 1476583 | n.2926G>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476597 | n.2940G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476616 | n.2959A>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| inhA | 1674471 | c.270G>T | synonymous_variant | 0.84 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674480 | c.279T>C | synonymous_variant | 0.87 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674486 | c.285T>C | synonymous_variant | 0.85 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674489 | c.288G>C | synonymous_variant | 0.87 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674491 | p.Phe97Tyr | missense_variant | 0.88 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674502 | p.Thr101Ser | missense_variant | 0.91 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674507 | c.306G>C | synonymous_variant | 0.91 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674534 | c.333G>T | synonymous_variant | 0.95 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674539 | p.Tyr113Phe | missense_variant | 0.95 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674542 | p.Ala114Glu | missense_variant | 0.95 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674546 | c.345T>C | synonymous_variant | 0.94 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674549 | c.348G>C | synonymous_variant | 0.95 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674561 | c.360C>T | synonymous_variant | 0.97 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674576 | c.375T>C | synonymous_variant | 0.97 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674585 | c.384T>G | synonymous_variant | 0.97 | isoniazid | Not assoc w R - Interim |
| ethionamide | Not assoc w R - Interim | |||||
| inhA | 1674589 | p.Met130Leu | missense_variant | 0.97 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674600 | c.399G>C | synonymous_variant | 0.97 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674601 | p.Leu134Thr | missense_variant | 0.96 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674619 | p.Pro140Ser | missense_variant | 0.95 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674624 | c.423A>C | synonymous_variant | 0.95 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674627 | c.426T>C | synonymous_variant | 0.95 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674630 | c.429C>G | synonymous_variant | 0.95 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674656 | p.Ser152Thr | missense_variant | 0.95 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674658 | c.457C>A | synonymous_variant | 0.95 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674669 | c.468G>C | synonymous_variant | 0.96 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674687 | c.486G>C | synonymous_variant | 0.97 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674703 | c.502_504delTTGinsCTC | synonymous_variant | 0.96 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674714 | c.513C>G | synonymous_variant | 0.96 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674718 | c.517_519delAGGinsCGA | synonymous_variant | 0.95 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674723 | c.522C>T | synonymous_variant | 0.97 | isoniazid | Not assoc w R - Interim |
| ethionamide | Not assoc w R - Interim | |||||
| inhA | 1674726 | c.525G>C | synonymous_variant | 0.97 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674732 | c.531C>T | synonymous_variant | 0.97 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674738 | c.537C>G | synonymous_variant | 0.97 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674742 | p.Lys181Pro | missense_variant | 0.97 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674750 | c.549T>G | synonymous_variant | 0.98 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674756 | c.555T>G | synonymous_variant | 0.98 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674759 | c.558G>C | synonymous_variant | 0.98 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674774 | c.573A>C | synonymous_variant | 0.99 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674777 | c.576C>G | synonymous_variant | 0.98 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674780 | c.579T>G | synonymous_variant | 0.99 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674786 | c.585G>C | synonymous_variant | 0.99 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674801 | c.600T>C | synonymous_variant | 0.99 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674804 | c.603G>C | synonymous_variant | 0.99 | isoniazid | |
| ethionamide | Not assoc w R - Interim | |||||
| inhA | 1674831 | p.Glu210Asp | missense_variant | 0.97 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674838 | p.Ala213Asn | missense_variant | 0.95 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674852 | c.651G>C | synonymous_variant | 0.98 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674858 | c.657G>A | synonymous_variant | 0.97 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674861 | c.660G>A | synonymous_variant | 0.98 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674879 | c.678T>A | synonymous_variant | 1.0 | isoniazid | |
| ethionamide |
