Run ID: SRR13861703
Sample name:
Date: 2024-10-05T08:58:32.267717
Number of reads: 331214
Percentage reads mapped: 16.58
Median coverage: 11.0
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 |
|---|---|---|---|---|---|---|
| gyrB | 5210 | c.-30C>G | upstream_gene_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| fgd1 | 490574 | c.-209G>C | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| ccsA | 620747 | p.Gly286Val | missense_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| rpsL | 781927 | p.Lys123Met | missense_variant | 1.0 | streptomycin | |
| Rv1129c | 1253316 | p.Gly407Ser | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | ||||||
| isoniazid | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| fbiC | 1304806 | p.Pro626Thr | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.87 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.88 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.88 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.88 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.88 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.88 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.9 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.9 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.9 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.88 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.87 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.87 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.87 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.87 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.87 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.87 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.86 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.86 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.85 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.83 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.53 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rpsA | 1834614 | p.Ile358Ser | missense_variant | 1.0 | pyrazinamide | |
| tsnR | 1853786 | c.181T>C | synonymous_variant | 1.0 | linezolid | |
| PPE35 | 2169834 | p.Gly260Val | missense_variant | 1.0 | pyrazinamide | |
| kasA | 2518887 | p.Gly258Val | missense_variant | 1.0 | isoniazid | |
| Rv2477c | 2782523 | p.Thr507Met | missense_variant | 1.0 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| Rv2477c | 2784377 | c.-335T>C | upstream_gene_variant | 1.0 | kanamycin | |
| levofloxacin | ||||||
| moxifloxacin | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| amikacin | ||||||
| pepQ | 2859750 | c.669C>T | synonymous_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| lpqB | 3623317 | p.Gln532Glu | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| glpK | 4139251 | p.Gly169Cys | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| streptomycin | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| embB | 4246876 | c.363G>A | synonymous_variant | 1.0 | ethambutol | |
| embB | 4248914 | p.Ala801Thr | missense_variant | 1.0 | ethambutol | Uncertain significance |
