Run ID: SRR22251647
Sample name:
Date: 2024-04-14T06:44:14.135824
Number of reads: 3110316
Percentage reads mapped: 99.63
Median coverage: 103.0
Strain: lineage4.3.3
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage4.3 | Euro-American (LAM) | None | 1.0 |
| lineage4 | Euro-American | None | 1.0 |
| lineage4.3.3 | Euro-American (LAM) | RD115 | 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 | 6408 | p.Glu390Gly | missense_variant | 1.0 | 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 | 8040 | p.Gly247Ser | 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 | |||||
| mshA | 576108 | p.Ala254Gly | missense_variant | 0.18 | ethionamide | |
| isoniazid | ||||||
| mshA | 576453 | p.Val369Gly | missense_variant | 0.18 | ethionamide | |
| isoniazid | ||||||
| mshA | 576468 | p.Val374Gly | missense_variant | 0.26 | ethionamide | |
| isoniazid | ||||||
| ccsA | 619640 | c.-251G>C | upstream_gene_variant | 0.99 | capreomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| rpoC | 764995 | c.1626C>G | synonymous_variant | 0.99 | rifampicin | Not assoc w R |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpS5 | 779514 | c.-609A>G | upstream_gene_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| 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 |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| kasA | 2518919 | p.Gly269Ser | missense_variant | 0.99 | isoniazid | |
| Rv2477c | 2784204 | c.-162A>C | upstream_gene_variant | 0.45 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2477c | 2784211 | c.-170_-169delGAinsCC | upstream_gene_variant | 0.47 | ethambutol | |
| moxifloxacin | ||||||
| streptomycin | ||||||
| levofloxacin | ||||||
| kanamycin | ||||||
| rifampicin | ||||||
| amikacin | ||||||
| Rv2752c | 3065824 | p.Pro123Leu | missense_variant | 1.0 | ethambutol | Not assoc w R |
| moxifloxacin | Uncertain significance | |||||
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R - Interim | |||||
| thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| fbiD | 3339716 | p.Gln200Pro | missense_variant | 0.16 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| whiB7 | 3568425 | c.255T>G | synonymous_variant | 0.29 | streptomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| whiB7 | 3568428 | c.252A>C | synonymous_variant | 0.23 | streptomycin | |
| amikacin | ||||||
| kanamycin | ||||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.99 | pyrazinamide | Not assoc w R |
| glpK | 4138820 | p.Asn312Lys | missense_variant | 1.0 | ethambutol | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| levofloxacin | ||||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| embC | 4240413 | p.Leu184Arg | missense_variant | 0.15 | ethambutol | |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4247028 | p.Leu172Arg | missense_variant | 0.36 | ethambutol | |
| ubiA | 4269300 | c.534G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| whiB6 | 4338312 | c.209_210insT | frameshift_variant | 0.95 | capreomycin | Uncertain significance |
| amikacin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| 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 | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |
