Run ID: SRR6936634
Sample name:
Date: 2024-03-25T22:43:18.303541
Number of reads: 488110
Percentage reads mapped: 99.77
Median coverage: 28.0
Strain: lineage4
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
c.702delG | Assoc w R | High-level resistance | ||
ethambutol | embB | p.Gly406Cys | Assoc w R | |
pyrazinamide | ||||
streptomycin | gid | c.102delG | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | fbiB | c.402delC | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
katG | 2155409 | c.702delG | frameshift_variant | 0.38 | isoniazid | Assoc w R | High-level resistance |
fbiB | 3641934 | c.402delC | frameshift_variant | 0.23 | delamanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance |
pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance | |||||
embB | 4247729 | p.Gly406Cys | missense_variant | 1.0 | ethambutol | Assoc w R | |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
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 | 8147 | p.Asn282Lys | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
gyrA | 8553 | c.1255delG | frameshift_variant | 0.2 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.97 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
ccsA | 620178 | c.288G>C | synonymous_variant | 1.0 | capreomycin | |
amikacin | Not assoc w R - Interim | |||||
kanamycin | Not assoc w R - Interim | |||||
rpoC | 764818 | c.1449G>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 767149 | c.3782delG | frameshift_variant | 0.4 | rifampicin | |
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 |
Rv1129c | 1254473 | c.61delC | frameshift_variant | 0.18 | moxifloxacin | Uncertain significance |
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
fbiC | 1304501 | p.Ala524Gly | missense_variant | 0.97 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
fbiC | 1305357 | c.2427C>G | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
tsnR | 1853666 | c.63delG | frameshift_variant | 0.69 | linezolid | Uncertain significance |
tsnR | 1853697 | c.96delC | frameshift_variant | 0.41 | linezolid | Uncertain significance |
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 |
ndh | 2102292 | c.750delC | frameshift_variant | 0.24 | ethionamide | Uncertain significance |
delamanid | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
PPE35 | 2170209 | c.403delG | frameshift_variant | 0.67 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
folC | 2747734 | c.-137delG | upstream_gene_variant | 0.18 | para-aminosalicylic_acid | |
Rv2681 | 2996916 | c.181delG | frameshift_variant | 0.32 | capreomycin | Uncertain significance |
whiB7 | 3568918 | c.-240delC | upstream_gene_variant | 0.48 | streptomycin | |
amikacin | ||||||
kanamycin | ||||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
clpC1 | 4038911 | c.1793delC | frameshift_variant | 0.25 | pyrazinamide | |
embC | 4239437 | c.-426T>C | upstream_gene_variant | 1.0 | ethambutol | Uncertain significance |
embC | 4241300 | c.1440delC | frameshift_variant | 0.24 | ethambutol | |
embC | 4242622 | c.2762delG | frameshift_variant | 0.5 | ethambutol | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243185 | c.-47delC | upstream_gene_variant | 0.33 | ethambutol | |
embA | 4243791 | c.562delC | frameshift_variant | 0.39 | ethambutol | Uncertain significance |
embA | 4244566 | c.1336delC | frameshift_variant | 0.35 | ethambutol | Uncertain significance |
aftB | 4267948 | c.888delC | frameshift_variant | 0.44 | ethambutol | Uncertain significance |
aftB | 4268343 | c.493delC | frameshift_variant | 0.29 | ethambutol | Uncertain significance |
ethA | 4327376 | p.Ala33Gly | missense_variant | 1.0 | ethionamide | 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 |