Run ID: ERR6197031
Sample name:
Date: 2024-04-16T12:48:24.420844
Number of reads: 1384091
Percentage reads mapped: 95.15
Median coverage: 44.0
Strain: lineage4.7
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.7 | Euro-American (mainly T) | None | 0.99 |
lineage4 | Euro-American | 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 | 1126 | c.1126C>T | synonymous_variant | 0.94 | isoniazid | Not assoc w R - Interim |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.18 | rifampicin | |
rpoB | 762995 | c.3189G>T | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoB | 763005 | p.Cys1067Val | missense_variant | 0.18 | rifampicin | |
rpoC | 763013 | c.-357C>A | upstream_gene_variant | 0.15 | rifampicin | |
rpoC | 763022 | c.-348C>A | upstream_gene_variant | 0.15 | rifampicin | |
rpoB | 763028 | c.3222T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 763052 | c.-318G>C | upstream_gene_variant | 0.15 | rifampicin | |
rpoB | 763053 | c.3247T>C | synonymous_variant | 0.17 | rifampicin | Not assoc w R - Interim |
rpoB | 763070 | c.3264T>C | synonymous_variant | 0.16 | rifampicin | Not assoc w R - Interim |
rpoB | 763074 | p.Thr1090Val | missense_variant | 0.14 | rifampicin | |
rpoB | 763085 | c.3279C>T | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoB | 763094 | c.3288G>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 763103 | c.-267G>A | upstream_gene_variant | 0.12 | rifampicin | |
rpoC | 763109 | c.-261C>G | upstream_gene_variant | 0.1 | rifampicin | |
rpoB | 763115 | c.3309T>C | synonymous_variant | 0.1 | rifampicin | Not assoc w R - Interim |
rpoC | 763546 | c.177A>G | synonymous_variant | 0.1 | rifampicin | Not assoc w R - Interim |
rpoC | 763570 | c.201G>C | synonymous_variant | 0.11 | rifampicin | Not assoc w R - Interim |
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 |
rpsL | 781443 | c.-117T>G | upstream_gene_variant | 1.0 | streptomycin | |
Rv1258c | 1407604 | c.-264C>T | upstream_gene_variant | 1.0 | streptomycin | |
isoniazid | ||||||
pyrazinamide | ||||||
rrs | 1473121 | n.1276T>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.94 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.94 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.97 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
PPE35 | 2170675 | c.-63G>C | upstream_gene_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
pepQ | 2859961 | p.Ala153Gly | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4249732 | c.3219C>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R |