Run ID: SRR25515459
Sample name:
Date: 2024-03-26T13:13:20.247319
Number of reads: 7619693
Percentage reads mapped: 99.58
Median coverage: 260.0
Strain: lineage4.4.2
Spoligotype:
Drug-resistance: Other
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4 | Euro-American | None | 1.0 |
| lineage4.4 | Euro-American | None | 0.99 |
| lineage4.4.2 | Euro-American | None | 0.99 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | rrs | n.517C>T | Assoc w R | |
| 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 |
|---|---|---|---|---|---|---|---|
| rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 1.0 | streptomycin | Assoc w R |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 6031 | c.792C>T | synonymous_variant | 0.98 | levofloxacin | |
| moxifloxacin | ||||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| fgd1 | 490824 | c.42A>G | synonymous_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| Rv1129c | 1253456 | p.Gly360Val | missense_variant | 1.0 | moxifloxacin | Uncertain significance |
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrs | 1472121 | n.276C>T | non_coding_transcript_exon_variant | 0.99 | streptomycin | Uncertain significance |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| inhA | 1673952 | c.-250G>A | upstream_gene_variant | 0.99 | ethionamide | |
| isoniazid | ||||||
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| katG | 2155214 | p.Trp300Arg | missense_variant | 1.0 | isoniazid | Uncertain significance |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| eis | 2714570 | p.Ala255Ser | missense_variant | 0.98 | amikacin | |
| kanamycin | ||||||
| Rv2681 | 2996608 | c.-131A>G | upstream_gene_variant | 1.0 | capreomycin | |
| Rv2752c | 3066099 | p.Met31Ile | missense_variant | 0.99 | ethambutol | Not assoc w R |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R - Interim | |||||
| ald | 3086712 | c.-108C>A | upstream_gene_variant | 1.0 | cycloserine | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3083 | 3448348 | c.-156G>A | upstream_gene_variant | 1.0 | ethionamide | |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| fbiA | 3640316 | c.-227_-226insT | upstream_gene_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| rpoA | 3878349 | c.159C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| clpC1 | 4038565 | p.Asp714Asn | missense_variant | 0.99 | pyrazinamide | |
| glpK | 4139183 | c.572dupG | frameshift_variant | 0.63 | ethambutol | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| embC | 4238963 | c.-900C>T | upstream_gene_variant | 0.99 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 0.99 | ethambutol | Not assoc w R |
| embA | 4246508 | c.3276G>A | synonymous_variant | 0.99 | ethambutol | Not assoc w R |
| ubiA | 4268928 | c.906C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269375 | c.459G>A | synonymous_variant | 0.99 | ethambutol | Not assoc w R |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
| amikacin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| gid | 4407535 | p.Thr223Met | missense_variant | 0.98 | streptomycin |
