TB-Profiler result

Run: ERR11465035
Summary

Run ID: ERR11465035

Sample name:

Date: 2024-04-15T03:51:27.749570

Number of reads: 8183274

Percentage reads mapped: 99.77

Median coverage: 234.0

Strain: lineage4.3.4.2;lineage4.4.1.1

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 0.53
lineage4.4.1 Euro-American (S-type) None 0.55
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.52
lineage4.3.4 Euro-American (LAM) RD174 0.5
lineage4.3.4.2 Euro-American (LAM) RD174 0.5
lineage4.4 Euro-American None 0.54
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid inhA c.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin gid c.351delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
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
inhA 1674048 c.-154G>A upstream_gene_variant 0.46 isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
gid 4407851 c.351delG frameshift_variant 0.47 streptomycin 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
gyrB 6817 c.1578G>A synonymous_variant 0.54 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
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 9138 p.Gln613Glu missense_variant 0.46 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
mshA 576108 p.Ala254Gly missense_variant 0.19 ethionamide
isoniazid
rpoC 764995 c.1626C>G synonymous_variant 0.5 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777416 c.1065G>T synonymous_variant 0.44 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
ndh 2102990 p.Val18Ala missense_variant 0.46 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
katG 2156815 c.-704A>G upstream_gene_variant 0.53 isoniazid
PPE35 2168479 p.Thr712Pro missense_variant 0.37 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.58 pyrazinamide 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
thyA 3073868 p.Thr202Ala missense_variant 0.51 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.54 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 0.54 streptomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
Rv3236c 3612009 p.Ala370Thr missense_variant 0.51 pyrazinamide Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.64 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.42 pyrazinamide Not assoc w R
clpC1 4040486 c.219G>A synonymous_variant 0.47 pyrazinamide
embC 4238963 c.-900C>T upstream_gene_variant 0.45 ethambutol Not assoc w R
embC 4239763 c.-100C>T upstream_gene_variant 0.51 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338592 c.-71G>C upstream_gene_variant 0.62 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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 4408156 p.Leu16Arg missense_variant 0.54 streptomycin Not assoc w R