TB-Profiler result

Run: ERR6358721
Summary

Run ID: ERR6358721

Sample name:

Date: 2024-04-14T19:00:42.590245

Number of reads: 1859732

Percentage reads mapped: 99.68

Median coverage: 53.0

Strain: lineage4.6.1.2;lineage4.6.5

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6.5 Euro-American None 0.57
lineage4.6 Euro-American None 1.0
lineage4.6.1.2 Euro-American RD724 0.33
lineage4 Euro-American None 1.0
lineage4.6.1 Euro-American (Uganda) RD724 0.33
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Gln10* Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA p.Asn236Lys Assoc w R
kanamycin
cycloserine
ethionamide ethA c.1215_1224delGTTGAATTAC Assoc w R
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761155 p.Ser450Leu missense_variant 0.26 rifampicin Assoc w R
tlyA 1918647 p.Asn236Lys missense_variant 0.68 capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.29 isoniazid Assoc w R High-level resistance
pncA 2289214 p.Gln10* stop_gained 0.37 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.39 ethambutol Assoc w R
ethA 4326249 c.1215_1224delGTTGAATTAC frameshift_variant 0.35 ethionamide Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
dnaA 1186 p.Glu396Lys missense_variant 0.62 isoniazid Uncertain significance
dnaA 1326 p.Gln442His missense_variant 0.76 isoniazid Uncertain significance
gyrB 5489 p.Ile84Val missense_variant 0.79 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7539 p.Thr80Ala missense_variant 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
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
fgd1 490756 c.-27T>G upstream_gene_variant 0.58 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491134 p.Tyr118His missense_variant 0.68 clofazimine
pretomanid
delamanid
rpoB 761406 p.Val534Met missense_variant 0.18 rifampicin Uncertain significance
rpoC 764703 p.Lys445Arg missense_variant 0.17 rifampicin Uncertain significance
rpoC 764810 p.Pro481Thr missense_variant 0.43 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 0.6 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
embR 1416410 p.Leu313Arg missense_variant 0.42 ethambutol Uncertain significance
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 2170692 c.-80T>G upstream_gene_variant 0.3 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 2714308 p.Pro342Leu missense_variant 0.42 amikacin Uncertain significance
kanamycin Uncertain significance
folC 2746995 p.Val202Ile missense_variant 0.56 para-aminosalicylic_acid
Rv2681 2996876 c.138A>C synonymous_variant 0.39 capreomycin Not assoc w R
Rv2752c 3065920 p.Pro91Leu missense_variant 0.27 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
whiB7 3569029 c.-350A>G upstream_gene_variant 0.21 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Not assoc w R
fbiA 3640346 c.-196delA upstream_gene_variant 0.74 clofazimine
pretomanid
delamanid
clpC1 4038332 c.2373C>T synonymous_variant 0.74 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245055 p.Thr608Asn missense_variant 0.33 ethambutol 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
gid 4408094 p.Gly37Arg missense_variant 0.32 streptomycin Uncertain significance