Run ID: ERR1200604
Sample name:
Date: 2024-04-14T09:23:59.888597
Number of reads: 8540753
Percentage reads mapped: 97.03
Median coverage: 61.0
Strain: lineage7
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage7 | Lineage 7 | 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 |
|---|---|---|---|---|---|---|
| dnaA | 1453 | p.Ala485Thr | missense_variant | 0.99 | isoniazid | 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 | 8876 | c.1575C>T | synonymous_variant | 1.0 | levofloxacin | |
| moxifloxacin | ||||||
| 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 | 13445 | c.114G>A | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| Rv0010c | 13563 | c.-5A>G | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
| pretomanid | ||||||
| delamanid | Not assoc w R - Interim | |||||
| Rv0565c | 656656 | p.Ala272Val | missense_variant | 1.0 | ethionamide | Uncertain significance |
| Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 1.0 | ethionamide | |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| rpoC | 764013 | p.Glu215Ala | missense_variant | 1.0 | rifampicin | Uncertain significance |
| rpoC | 766955 | p.Glu1196Lys | missense_variant | 1.0 | rifampicin | Uncertain significance |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| mmpL5 | 776202 | p.Gly760Ala | missense_variant | 1.0 | clofazimine | |
| bedaquiline | ||||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| rpsL | 781488 | c.-72G>A | upstream_gene_variant | 1.0 | streptomycin | |
| Rv1129c | 1253707 | c.828A>C | synonymous_variant | 1.0 | moxifloxacin | |
| levofloxacin | ||||||
| rifampicin | Not assoc w R - Interim | |||||
| isoniazid | Not assoc w R - Interim | |||||
| Rv1129c | 1254136 | p.Glu133Asp | missense_variant | 1.0 | moxifloxacin | Uncertain significance |
| levofloxacin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | moxifloxacin | Not assoc w R |
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| fbiC | 1305129 | c.2199C>T | synonymous_variant | 1.0 | clofazimine | |
| pretomanid | ||||||
| delamanid | ||||||
| embR | 1416977 | p.His124Arg | missense_variant | 1.0 | ethambutol | Uncertain significance |
| embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
| kanamycin | ||||||
| capreomycin | ||||||
| amikacin | ||||||
| rrl | 1474959 | n.1303_1304insAC | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
| linezolid | ||||||
| rpsA | 1834916 | p.Thr459Pro | missense_variant | 1.0 | pyrazinamide | |
| 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 |
| tlyA | 1918281 | c.342A>C | synonymous_variant | 1.0 | capreomycin | |
| bacA | 2062922 | p.Ile603Val | missense_variant | 1.0 | streptomycin | Not assoc w R |
| kanamycin | Not assoc w R | |||||
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| ndh | 2102218 | c.825C>T | synonymous_variant | 1.0 | ethionamide | |
| delamanid | ||||||
| isoniazid | Not assoc w R - Interim | |||||
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| PPE35 | 2169232 | p.Thr461Ala | missense_variant | 1.0 | pyrazinamide | |
| Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| Rv2681 | 2998027 | p.Ala430Val | missense_variant | 1.0 | capreomycin | |
| Rv2752c | 3065880 | c.312C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| levofloxacin | Not assoc w R - Interim | |||||
| rifampicin | Not assoc w R - Interim | |||||
| isoniazid | Not assoc w R - Interim | |||||
| ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
| Rv3083 | 3448540 | p.Gly13Ser | missense_variant | 1.0 | ethionamide | |
| Rv3236c | 3612100 | c.1017C>T | synonymous_variant | 1.0 | pyrazinamide | |
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
| rifampicin | Not assoc w R | |||||
| mtrB | 3627386 | c.-774delC | upstream_gene_variant | 1.0 | bedaquiline | |
| rifampicin | ||||||
| rpoA | 3878040 | c.468T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
| glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| levofloxacin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| embC | 4240153 | c.291G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| embC | 4240922 | p.Thr354Ala | missense_variant | 1.0 | ethambutol | |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4248073 | c.1560C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| aftB | 4267649 | c.1188T>C | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269606 | c.228T>C | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ethA | 4328371 | c.-898C>T | upstream_gene_variant | 1.0 | ethionamide | |
| 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 | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
