Run ID: SRR13837522
Sample name:
Date: 2024-10-05T13:01:37.336264
Number of reads: 587586
Percentage reads mapped: 97.0
Median coverage: 20.0
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 |
|---|---|---|---|---|---|---|
| fgd1 | 490804 | p.Tyr8Asn | missense_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| fgd1 | 490893 | c.111C>T | synonymous_variant | 1.0 | pretomanid | |
| delamanid | ||||||
| clofazimine | ||||||
| mshA | 575498 | p.Ala51Pro | missense_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| Rv0565c | 656747 | p.Val242Ile | missense_variant | 1.0 | ethionamide | |
| Rv0565c | 656828 | p.Tyr215His | missense_variant | 1.0 | ethionamide | |
| rpoC | 763663 | c.294C>A | synonymous_variant | 1.0 | rifampicin | |
| rpoC | 763955 | p.Lys196Gln | missense_variant | 1.0 | rifampicin | |
| rpoC | 765682 | p.Asn771Lys | missense_variant | 1.0 | rifampicin | |
| rpoC | 766342 | c.2973C>A | synonymous_variant | 1.0 | rifampicin | |
| rpsL | 781579 | p.Leu7Arg | missense_variant | 1.0 | streptomycin | |
| Rv1129c | 1254119 | p.Ser139Phe | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| embR | 1416509 | p.Arg280Pro | missense_variant | 1.0 | ethambutol | |
| rrl | 1474164 | n.507C>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| inhA | 1674315 | c.114C>G | synonymous_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| katG | 2154959 | c.1153C>A | synonymous_variant | 1.0 | isoniazid | |
| PPE35 | 2170236 | c.376_377insG | frameshift_variant | 1.0 | pyrazinamide | Uncertain significance |
| pncA | 2290061 | c.-820C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| folC | 2747798 | c.-200A>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| pepQ | 2860252 | p.Thr56Ser | missense_variant | 1.0 | bedaquiline | |
| clofazimine | ||||||
| Rv2680 | 2996652 | p.Val183Ala | missense_variant | 1.0 | capreomycin | |
| Rv2752c | 3065651 | p.Arg181Gly | missense_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| isoniazid | ||||||
| rifampicin | ||||||
| ethambutol | ||||||
| Rv3083 | 3448855 | p.Val118Ile | missense_variant | 1.0 | ethionamide | |
| whiB7 | 3569074 | c.-395A>G | upstream_gene_variant | 1.0 | kanamycin | |
| amikacin | ||||||
| streptomycin | ||||||
| mtrB | 3626557 | p.Met19Ile | missense_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| mtrB | 3626629 | c.-17_-16insT | upstream_gene_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| rpoA | 3877765 | p.Ala248Gly | missense_variant | 1.0 | rifampicin | |
| panD | 4044948 | c.-667A>G | upstream_gene_variant | 1.0 | pyrazinamide | |
| embB | 4247059 | c.546C>G | synonymous_variant | 1.0 | ethambutol | |
| embB | 4247144 | p.Ser211Pro | missense_variant | 1.0 | ethambutol | |
| ubiA | 4269553 | p.Ala94Gly | missense_variant | 1.0 | ethambutol | |
| gid | 4408259 | c.-57G>C | upstream_gene_variant | 1.0 | streptomycin |
