Run ID: SRR13861337
Sample name:
Date: 2024-10-05T08:58:20.911436
Number of reads: 587919
Percentage reads mapped: 14.71
Median coverage: 19.0
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 |
|---|---|---|---|---|---|---|
| dnaA | 715 | p.Thr239Pro | missense_variant | 1.0 | isoniazid | |
| fgd1 | 490955 | p.Met58Arg | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| mshA | 574818 | c.-530G>C | upstream_gene_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| hadA | 731861 | c.-69G>C | upstream_gene_variant | 1.0 | isoniazid | |
| rpsL | 781155 | c.-405G>A | upstream_gene_variant | 1.0 | streptomycin | |
| fbiC | 1304529 | c.1599T>C | synonymous_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| Rv1258c | 1406845 | p.Ala166Pro | missense_variant | 1.0 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.74 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.79 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.79 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.79 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.79 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.82 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.79 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.79 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.81 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.8 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.8 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.8 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.8 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.8 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.83 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.82 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.77 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.78 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.76 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.76 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.43 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
| linezolid | ||||||
| inhA | 1674607 | p.Pro136Ser | missense_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| inhA | 1674778 | p.Pro193Ala | missense_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| rpsA | 1833269 | c.-273G>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| bacA | 2064115 | p.Ala205Asp | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| PPE35 | 2169081 | p.Leu511Ser | missense_variant | 1.0 | pyrazinamide | |
| PPE35 | 2169202 | p.Ser471Pro | missense_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2222091 | c.1074G>T | synonymous_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv1979c | 2223306 | c.-142T>A | upstream_gene_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| pncA | 2289228 | p.Ile5Asn | missense_variant | 1.0 | pyrazinamide | |
| kasA | 2518176 | p.Ala21Gly | missense_variant | 1.0 | isoniazid | |
| eis | 2714755 | p.Pro193Gln | missense_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| ahpC | 2726324 | c.132A>G | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| ahpC | 2726362 | p.Phe57Ser | missense_variant | 1.0 | isoniazid | |
| pepQ | 2859580 | p.Leu280Arg | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| pepQ | 2859999 | c.420G>T | synonymous_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| thyA | 3074620 | c.-149C>A | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| mtrB | 3626051 | p.Ser188Trp | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| ddn | 3986889 | p.Phe16Val | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| embC | 4242041 | p.Met727Leu | missense_variant | 1.0 | ethambutol | |
| embA | 4244723 | p.Gln497His | missense_variant | 1.0 | ethambutol | Uncertain significance |
| aftB | 4267979 | c.858G>C | synonymous_variant | 1.0 | ethambutol |
