Run ID: SRR28046141
Sample name:
Date: 2024-05-22T09:56:51.761491
Number of reads: 8101509
Percentage reads mapped: 99.52
Median coverage: 218.0
Strain: lineage4.4
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Asp435Val | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Asp354Ala | Assoc w R | |
pyrazinamide | pncA | p.Thr100Pro | Assoc w R - Interim | |
p.Thr76Pro | Assoc w R | |||
c.-11A>G | Assoc w R | |||
streptomycin | gid | c.115delC | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Gly | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Gly | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.237dupG | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | moxifloxacin | Assoc w R | High-level resistance |
levofloxacin | Assoc w R | ||||||
rpoB | 761110 | p.Asp435Val | missense_variant | 0.98 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288944 | p.Thr100Pro | missense_variant | 0.22 | pyrazinamide | Assoc w R - Interim | |
pncA | 2289016 | p.Thr76Pro | missense_variant | 0.29 | pyrazinamide | Assoc w R | |
pncA | 2289252 | c.-11A>G | upstream_gene_variant | 0.41 | pyrazinamide | Assoc w R | |
embB | 4247574 | p.Asp354Ala | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4327236 | c.237dupG | frameshift_variant | 1.0 | ethionamide | Assoc w R | |
gid | 4408087 | c.115delC | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
rpoB | 760315 | p.Val170Gly | 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 | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rrs | 1471618 | n.-228G>C | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
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 |
PPE35 | 2170558 | p.Ala19Pro | missense_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 | |||||
eis | 2714523 | p.His270Gln | missense_variant | 1.0 | amikacin | Uncertain significance |
kanamycin | Uncertain significance | |||||
ahpC | 2726762 | c.570C>G | synonymous_variant | 1.0 | isoniazid | |
folC | 2747480 | p.Glu40Val | missense_variant | 1.0 | para-aminosalicylic_acid | |
pepQ | 2859521 | c.898C>T | synonymous_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
Rv2752c | 3065715 | c.477T>C | 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 | |||||
Rv2752c | 3066452 | c.-261T>G | upstream_gene_variant | 1.0 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448946 | c.445dupT | frameshift_variant | 1.0 | ethionamide | Uncertain significance |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.99 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
rpoA | 3878619 | c.-112A>C | upstream_gene_variant | 0.17 | rifampicin | |
embC | 4238963 | c.-900C>T | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243324 | p.Val31Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.25 | ethambutol | |
embB | 4247039 | p.Phe176Val | missense_variant | 0.12 | ethambutol | |
embB | 4247548 | c.1035C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
ubiA | 4268928 | c.906C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269375 | c.459G>A | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4326509 | p.Ala322Val | 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 |