Run ID: SRR13861441
Sample name:
Date: 2024-04-15T22:29:43.556303
Number of reads: 1450805
Percentage reads mapped: 24.2
Median coverage: 48.0
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 | 6561 | p.Lys441Arg | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7705 | p.Thr135Ser | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 8409 | p.Leu370Ile | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| Rv0010c | 13327 | p.Leu78Ile | missense_variant | 1.0 | isoniazid | |
| ccsA | 619637 | c.-254T>G | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| ccsA | 620157 | c.267G>T | synonymous_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| rplC | 801215 | c.408delC | frameshift_variant | 1.0 | linezolid | |
| Rv1129c | 1253639 | p.Leu299* | stop_gained | 1.0 | moxifloxacin | Uncertain significance |
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| fbiC | 1304409 | c.1479C>G | synonymous_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| fbiC | 1304501 | p.Ala524Gly | missense_variant | 1.0 | clofazimine | Uncertain significance |
| pretomanid | ||||||
| delamanid | Uncertain significance | |||||
| sigE | 1365081 | c.669G>T | synonymous_variant | 1.0 | pyrazinamide | |
| rrs | 1472791 | n.946G>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
| kanamycin | Uncertain significance | |||||
| capreomycin | ||||||
| amikacin | Uncertain significance | |||||
| rrs | 1472990 | n.1145A>G | non_coding_transcript_exon_variant | 0.2 | streptomycin | Uncertain significance |
| kanamycin | Not assoc w R | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| rrs | 1473008 | n.1163C>A | non_coding_transcript_exon_variant | 0.19 | streptomycin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| capreomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.55 | capreomycin | |
| linezolid | ||||||
| rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.59 | capreomycin | |
| linezolid | ||||||
| rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.59 | capreomycin | |
| linezolid | ||||||
| rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.59 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.59 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.61 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.61 | capreomycin | |
| linezolid | ||||||
| rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.61 | capreomycin | |
| linezolid | ||||||
| rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.64 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.63 | capreomycin | |
| linezolid | ||||||
| rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.63 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.63 | capreomycin | |
| linezolid | ||||||
| rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.64 | capreomycin | |
| linezolid | ||||||
| rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.62 | capreomycin | |
| linezolid | ||||||
| rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.62 | capreomycin | |
| linezolid | ||||||
| rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.59 | capreomycin | |
| linezolid | ||||||
| rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.59 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.19 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| PPE35 | 2168564 | c.2049T>A | synonymous_variant | 1.0 | pyrazinamide | |
| kasA | 2519179 | c.1065G>C | synonymous_variant | 1.0 | isoniazid | |
| folC | 2746546 | p.Asp351Glu | missense_variant | 1.0 | para-aminosalicylic_acid | |
| Rv2477c | 2784407 | c.-365A>G | upstream_gene_variant | 1.0 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2680 | 2996063 | c.-42G>C | upstream_gene_variant | 1.0 | capreomycin | |
| thyX | 3068038 | c.-93C>A | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| Rv3083 | 3448608 | c.105G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| whiB7 | 3569032 | c.-353C>A | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| Rv3236c | 3612721 | c.396G>T | synonymous_variant | 1.0 | pyrazinamide | |
| fbiA | 3641221 | p.Pro227Ala | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| rpoA | 3879230 | c.-723C>G | upstream_gene_variant | 1.0 | rifampicin | |
| clpC1 | 4039647 | p.Glu353Ala | missense_variant | 1.0 | pyrazinamide | |
| clpC1 | 4040955 | c.-251A>C | upstream_gene_variant | 1.0 | pyrazinamide | |
| embC | 4239484 | c.-379T>C | upstream_gene_variant | 1.0 | ethambutol | |
| embC | 4240006 | c.144A>C | synonymous_variant | 1.0 | ethambutol | |
| embA | 4244074 | p.Ala281Val | missense_variant | 1.0 | ethambutol | |
| embA | 4245739 | p.Arg836His | missense_variant | 1.0 | ethambutol | |
| ethA | 4326731 | p.Ala248Gly | missense_variant | 1.0 | ethionamide | |
| ethR | 4327623 | c.75_76insC | frameshift_variant | 1.0 | ethionamide | Uncertain significance |
| gid | 4408334 | c.-132G>T | upstream_gene_variant | 1.0 | streptomycin |
