TB-Profiler result

Run: ERR4025129
Summary

Run ID: ERR4025129

Sample name:

Date: 2024-04-16T12:24:56.073682

Number of reads: 2017922

Percentage reads mapped: 99.63

Median coverage: 59.0

Strain: lineage4.1.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.34
lineage4.1 Euro-American None 0.65
lineage4.1.2 Euro-American None 0.6
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.63
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.34
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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
katG 2155168 p.Ser315Thr missense_variant 0.35 isoniazid Assoc w R High-level resistance
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
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 8040 p.Gly247Ser missense_variant 0.35 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 491591 p.Lys270Met missense_variant 0.62 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.63 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.66 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.51 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.46 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.61 rifampicin Not assoc w R
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 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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.76 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.38 isoniazid
Rv2477c 2783921 p.Gly41Glu missense_variant 0.3 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Not assoc w R
amikacin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.19 capreomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.49 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339040 c.-78T>C upstream_gene_variant 0.63 clofazimine
pretomanid
delamanid
mtrB 3625065 p.Met517Leu missense_variant 0.98 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627756 c.-407A>T upstream_gene_variant 0.66 bedaquiline
rifampicin
fbiA 3640393 c.-150A>C upstream_gene_variant 0.62 clofazimine
pretomanid
delamanid
clpC1 4038287 c.2418C>T synonymous_variant 0.27 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.71 ethambutol Not assoc w R
embC 4242182 p.Ala774Ser missense_variant 0.43 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.53 ethambutol Not assoc w R
embB 4248043 c.1530C>G synonymous_variant 0.54 ethambutol Not assoc w R - Interim
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
whiB6 4338901 c.-380T>G upstream_gene_variant 0.63 capreomycin
amikacin
kanamycin
gid 4407973 p.Val77Gly missense_variant 0.34 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.33 streptomycin Not assoc w R
gid 4408312 c.-110C>T upstream_gene_variant 0.56 streptomycin