Run ID: SRR13837626
Sample name:
Date: 2024-04-15T22:29:16.087035
Number of reads: 293734
Percentage reads mapped: 98.0
Median coverage: 10.0
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 | embR | p.Ser188Arg | Mutation from literature | |
| 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 |
|---|---|---|---|---|---|---|---|
| embR | 1416784 | p.Ser188Arg | missense_variant | 1.0 | ethambutol | Mutation from literature |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| fgd1 | 490771 | c.-12T>G | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| mshA | 575112 | c.-236G>T | upstream_gene_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| rpoB | 761125 | c.1320dupG | frameshift_variant | 1.0 | rifampicin | |
| fbiC | 1303334 | p.Gly135Val | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| embR | 1416250 | c.1098C>A | synonymous_variant | 1.0 | ethambutol | |
| rrl | 1474218 | n.561T>C | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rrl | 1475718 | n.2061T>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| fabG1 | 1673184 | c.-256T>C | upstream_gene_variant | 1.0 | ethionamide | |
| isoniazid | ||||||
| rpsA | 1833707 | p.Gly56Arg | missense_variant | 1.0 | pyrazinamide | |
| tlyA | 1918168 | p.Phe77Leu | missense_variant | 1.0 | capreomycin | |
| bacA | 2063427 | c.1302G>T | synonymous_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| ndh | 2103307 | c.-265A>G | upstream_gene_variant | 1.0 | ethionamide | |
| delamanid | ||||||
| isoniazid | ||||||
| kasA | 2518023 | c.-92C>T | upstream_gene_variant | 1.0 | isoniazid | |
| folC | 2747689 | c.-91C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
| fbiD | 3339289 | p.Ser58Ala | missense_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| whiB7 | 3569132 | c.-453C>T | upstream_gene_variant | 1.0 | streptomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| Rv3236c | 3613708 | c.-592C>G | upstream_gene_variant | 1.0 | pyrazinamide |
