Run ID: SRR13837875
Sample name:
Date: 2024-10-04T04:07:51.235312
Number of reads: 2939063
Percentage reads mapped: 95.03
Median coverage: 100.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
| 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 | fbiC | c.170dupA | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| c.1116delC | Assoc w R - Interim | Confers DLM-PMD cross-resistance | ||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|---|---|---|---|---|---|---|
| fbiC | 1303099 | c.170dupA | frameshift_variant | 0.99 | delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance | |||||
| fbiC | 1304043 | c.1116delC | frameshift_variant | 1.0 | delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrA | 9490 | p.Gly730Asp | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| Rv0010c | 13883 | c.-325T>A | upstream_gene_variant | 1.0 | isoniazid | |
| fgd1 | 491231 | p.Phe150Tyr | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| Rv0565c | 656020 | p.Gly484Val | missense_variant | 1.0 | ethionamide | |
| rpoC | 766128 | p.Ala920Gly | missense_variant | 1.0 | rifampicin | |
| rpsL | 781503 | c.-57T>C | upstream_gene_variant | 1.0 | streptomycin | |
| rplC | 800381 | c.-428A>G | upstream_gene_variant | 1.0 | linezolid | Uncertain significance |
| sigE | 1364655 | p.Met81Ile | missense_variant | 1.0 | pyrazinamide | |
| Rv1258c | 1406861 | p.Ile160Met | missense_variant | 1.0 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| Rv1258c | 1407463 | c.-123G>C | upstream_gene_variant | 1.0 | streptomycin | |
| pyrazinamide | ||||||
| isoniazid | ||||||
| rrs | 1472303 | n.458G>A | non_coding_transcript_exon_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrl | 1474235 | n.578G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1475139 | n.1482C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1476248 | n.2591G>A | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
| linezolid | ||||||
| rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.2 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.23 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.15 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.25 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.24 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.21 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476576 | n.2919C>G | non_coding_transcript_exon_variant | 0.94 | capreomycin | |
| linezolid | ||||||
| bacA | 2063299 | p.Trp477Leu | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| kasA | 2518209 | p.Thr32Arg | missense_variant | 1.0 | isoniazid | |
| folC | 2746788 | p.Ala271Pro | missense_variant | 1.0 | para-aminosalicylic_acid | |
| thyX | 3067214 | p.Ser244Arg | missense_variant | 1.0 | para-aminosalicylic_acid | |
| fbiD | 3339396 | c.279C>T | synonymous_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| mtrA | 3627293 | p.Glu19Asp | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| rpoA | 3878048 | p.Ala154Ser | missense_variant | 1.0 | rifampicin | |
| panD | 4044922 | c.-641G>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| glpK | 4139628 | p.Gln43Leu | missense_variant | 0.99 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| embB | 4248368 | p.Leu619Val | missense_variant | 1.0 | ethambutol | |
| ethA | 4327082 | p.Cys131Ser | missense_variant | 1.0 | ethionamide | |
| ethA | 4327097 | p.Leu126His | missense_variant | 1.0 | ethionamide | |
| gid | 4407792 | c.411G>C | synonymous_variant | 1.0 | streptomycin |
