Run ID: ERR3170462
Sample name:
Date: 2025-05-07T01:38:05.507360
Number of reads: 1681293
Percentage reads mapped: 99.47
Median coverage: 74.0
Strain: lineage6.3.3
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage6.3 | West-Africa 2 | RD702 | 1.0 |
| lineage6 | West-Africa 2 | RD702 | 1.0 |
| lineage6.3.3 | West-Africa 2 | RD702 | 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 | 6446 | p.Ala403Ser | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Uncertain significance | |||||
| gyrB | 7172 | p.Asp645Asn | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| 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 | 9143 | c.1842T>C | synonymous_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 | |||||
| Rv0010c | 13460 | c.99T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| Rv0010c | 13482 | p.Ala26Val | missense_variant | 1.0 | isoniazid | Not assoc w R |
| fgd1 | 491668 | p.Lys296Glu | missense_variant | 1.0 | clofazimine | Uncertain significance |
| delamanid | Uncertain significance | |||||
| pretomanid | Uncertain significance | |||||
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
| delamanid | Not assoc w R - Interim | |||||
| pretomanid | Uncertain significance | |||||
| ccsA | 619628 | c.-263G>A | upstream_gene_variant | 1.0 | amikacin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| Rv0565c | 656432 | p.Gly347Ser | missense_variant | 1.0 | ethionamide | Uncertain significance |
| Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 1.0 | ethionamide | Uncertain significance |
| nusG | 734151 | c.-103G>C | upstream_gene_variant | 1.0 | rifampicin | Uncertain significance |
| rpoB | 760969 | p.Ser388Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 761723 | p.Glu639Asp | missense_variant | 1.0 | rifampicin | Not assoc w R |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 764550 | p.Pro394Gln | missense_variant | 1.0 | rifampicin | Uncertain significance |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpL5 | 777075 | p.Ala469Val | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| clofazimine | Uncertain significance | |||||
| mmpL5 | 777485 | c.996T>C | synonymous_variant | 1.0 | bedaquiline | Uncertain significance |
| clofazimine | Uncertain significance | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| moxifloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
| delamanid | Uncertain significance | |||||
| pretomanid | Uncertain significance | |||||
| embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance |
| atpE | 1461251 | c.207G>T | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | amikacin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| inhA | 1674434 | p.Val78Ala | missense_variant | 1.0 | ethionamide | Uncertain significance |
| isoniazid | Not assoc w R | |||||
| 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 |
| bacA | 2062922 | p.Ile603Val | missense_variant | 1.0 | amikacin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| bacA | 2063121 | c.1608A>T | synonymous_variant | 1.0 | amikacin | Not assoc w R - Interim |
| capreomycin | Not assoc w R - Interim | |||||
| kanamycin | Not assoc w R - Interim | |||||
| streptomycin | Not assoc w R - Interim | |||||
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| katG | 2155503 | c.609C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| PPE35 | 2170250 | c.363G>A | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
| PPE35 | 2170345 | p.Ala90Pro | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
| PPE35 | 2170658 | c.-48_-47delCG | upstream_gene_variant | 1.0 | pyrazinamide | Uncertain significance |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | Uncertain significance |
| eis | 2714579 | c.754T>C | synonymous_variant | 1.0 | amikacin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| ald | 3086728 | c.-92C>T | upstream_gene_variant | 1.0 | cycloserine | Uncertain significance |
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | Uncertain significance |
| ald | 3087084 | c.266delA | frameshift_variant | 1.0 | cycloserine | Uncertain significance |
| Rv3083 | 3449781 | c.1278G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| whiB7 | 3568874 | c.-195C>T | upstream_gene_variant | 1.0 | amikacin | Uncertain significance |
| kanamycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| lpqB | 3624077 | c.834G>A | synonymous_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R - Interim | |||||
| lpqB | 3624350 | c.561G>T | synonymous_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| rifampicin | Not assoc w R | |||||
| lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| rpoA | 3877696 | p.Thr271Ile | missense_variant | 1.0 | rifampicin | Uncertain significance |
| glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
| isoniazid | Not assoc w R | |||||
| levofloxacin | Not assoc w R | |||||
| moxifloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| embC | 4240242 | p.Asn127Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4241843 | p.Leu661Ile | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4243904 | c.672G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| embA | 4244220 | c.988C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4244379 | p.Pro383Ser | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4246864 | c.351C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
| aftB | 4268477 | c.360C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| ubiA | 4269351 | c.483C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269522 | c.312C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269606 | c.228T>C | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ethA | 4326465 | p.Ile337Val | missense_variant | 1.0 | ethionamide | Uncertain significance |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | amikacin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| kanamycin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | amikacin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| kanamycin | Uncertain significance | |||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
