Run ID: SRR12006082
Sample name:
Date: 2024-10-04T20:48:03.098959
Number of reads: 7818445
Percentage reads mapped: 76.53
Median coverage: 162.0
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 |
|---|---|---|---|---|---|---|
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1473147 | n.1302G>A | non_coding_transcript_exon_variant | 0.11 | kanamycin | Uncertain significance |
| capreomycin | ||||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473150 | n.1305T>G | non_coding_transcript_exon_variant | 0.12 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473158 | n.1313T>C | non_coding_transcript_exon_variant | 0.12 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1473161 | n.1316A>C | non_coding_transcript_exon_variant | 0.12 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473164 | n.1319C>T | non_coding_transcript_exon_variant | 0.14 | kanamycin | |
| capreomycin | ||||||
| streptomycin | Uncertain significance | |||||
| amikacin | ||||||
| rrs | 1473172 | n.1327T>G | non_coding_transcript_exon_variant | 0.14 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1473173 | n.1328C>T | non_coding_transcript_exon_variant | 0.15 | kanamycin | Uncertain significance |
| capreomycin | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1473188 | n.1343T>C | non_coding_transcript_exon_variant | 0.21 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1473201 | n.1356A>C | non_coding_transcript_exon_variant | 0.21 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.21 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | ||||||
| amikacin | Uncertain significance | |||||
| rrs | 1473216 | n.1371C>T | non_coding_transcript_exon_variant | 0.22 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1473252 | n.1407T>C | non_coding_transcript_exon_variant | 0.12 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Not assoc w R | |||||
| rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476336 | n.2679C>G | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.33 | capreomycin | |
| linezolid | ||||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.34 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.39 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.4 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.4 | capreomycin | |
| linezolid | ||||||
| rrl | 1476423 | n.2766T>C | non_coding_transcript_exon_variant | 0.46 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476428 | n.2771C>A | non_coding_transcript_exon_variant | 0.44 | capreomycin | |
| linezolid | ||||||
| rrl | 1476458 | n.2801T>G | non_coding_transcript_exon_variant | 0.32 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.24 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| PPE35 | 2170598 | c.15G>A | synonymous_variant | 1.0 | pyrazinamide |
