Run ID: SRR13861614
Sample name:
Date: 2024-04-15T07:53:01.192745
Number of reads: 2393470
Percentage reads mapped: 47.92
Median coverage: 81.0
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 | 377 | p.Thr126Asn | missense_variant | 1.0 | isoniazid | |
| dnaA | 1519 | p.Arg507Ser | missense_variant | 1.0 | isoniazid | |
| gyrB | 5709 | p.Gly157Val | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 9028 | p.Val576Ala | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| Rv0565c | 657669 | c.-199C>A | upstream_gene_variant | 1.0 | ethionamide | |
| rpoB | 762011 | c.2205G>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| rpoB | 762279 | c.2474delA | frameshift_variant | 1.0 | rifampicin | |
| mmpS5 | 778823 | p.Ile28Thr | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rplC | 800279 | c.-530A>C | upstream_gene_variant | 1.0 | linezolid | |
| fbiC | 1304640 | c.1710A>C | synonymous_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| Rv1258c | 1406376 | p.Gly322Val | missense_variant | 1.0 | streptomycin | |
| isoniazid | ||||||
| pyrazinamide | ||||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.31 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.36 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.36 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.36 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.37 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.41 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.44 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.43 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.43 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.43 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.43 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.42 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.42 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.42 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.42 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.41 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.37 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.37 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.35 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.34 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.14 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| PPE35 | 2169882 | p.Ser244Ile | missense_variant | 0.99 | pyrazinamide | |
| eis | 2714940 | c.392delA | frameshift_variant | 1.0 | amikacin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| Rv2477c | 2782900 | c.1143C>G | synonymous_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| ald | 3087311 | c.492C>G | synonymous_variant | 1.0 | cycloserine | |
| Rv3236c | 3613629 | c.-513C>G | upstream_gene_variant | 1.0 | pyrazinamide | |
| fbiB | 3642465 | p.Asp311His | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| alr | 3840300 | p.Pro374His | missense_variant | 1.0 | cycloserine | |
| rpoA | 3878288 | p.Thr74Pro | missense_variant | 1.0 | rifampicin | |
| clpC1 | 4039415 | c.1289dupA | frameshift_variant | 1.0 | pyrazinamide | |
| clpC1 | 4040792 | c.-88A>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| embA | 4243235 | c.3G>T | synonymous_variant | 1.0 | ethambutol |
