Run ID: ERR1679638
Sample name:
Date: 2024-03-27T00:26:44.090551
Number of reads: 1008454
Percentage reads mapped: 99.78
Median coverage: 34.0
Strain: lineage4.6.5
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.6.5 | Euro-American | None | 1.0 |
lineage4.6 | Euro-American | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
rpoC | p.Phe452Ser | Uncertain significance | Mutation from literature | |
isoniazid | ||||
ethambutol | embA | c.-12C>T | Uncertain significance | Mutation from literature |
embB | p.Met306Ile | Assoc w R | ||
p.Ala313Val | Uncertain significance | Mutation from literature | ||
pyrazinamide | ||||
streptomycin | gid | c.294delC | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94His | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94His | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | tlyA | p.Asn236Lys | Assoc w R | |
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7581 | p.Asp94His | missense_variant | 1.0 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpoC | 764724 | p.Phe452Ser | missense_variant | 1.0 | rifampicin | Uncertain significance | Mutation from literature |
tlyA | 1918647 | p.Asn236Lys | missense_variant | 1.0 | capreomycin | Assoc w R | |
embA | 4243221 | c.-12C>T | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance | Mutation from literature |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol | Assoc w R | |
embB | 4247451 | p.Ala313Val | missense_variant | 1.0 | ethambutol | Uncertain significance | Mutation from literature |
gid | 4407908 | c.294delC | frameshift_variant | 1.0 | streptomycin | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1186 | p.Glu396Lys | missense_variant | 1.0 | isoniazid | Uncertain significance |
dnaA | 1326 | p.Gln442His | missense_variant | 0.98 | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
rpoB | 759604 | c.-203A>G | upstream_gene_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 | 777974 | c.507C>T | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
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 |
katG | 2155667 | p.Trp149Arg | missense_variant | 1.0 | isoniazid | Uncertain significance |
PPE35 | 2170007 | c.544_605delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG | frameshift_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 | |||||
pncA | 2288806 | p.Ala146Pro | missense_variant | 1.0 | pyrazinamide | |
folC | 2746995 | p.Val202Ile | missense_variant | 1.0 | para-aminosalicylic_acid | |
glpK | 4138929 | p.Glu276Gly | missense_variant | 1.0 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin |