TB-Profiler result

Run: ERR5897078
Summary

Run ID: ERR5897078

Sample name:

Date: 2024-06-18T07:59:38.013475

Number of reads: 10723846

Percentage reads mapped: 99.59

Median coverage: 285.0

Strain: lineage2.2.1;lineage4.9

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.1
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.11
lineage2.2 East-Asian (Beijing) RD105;RD207 0.09
lineage4 Euro-American None 0.89
lineage4.9 Euro-American (H37Rv-like) None 0.9
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 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)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Thr160Pro Assoc w R
p.Pro54Leu Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
ethA c.392delG 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
gyrA 7570 p.Ala90Val missense_variant 0.87 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.12 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.94 streptomycin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.16 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 amikacin Assoc w R
kanamycin Assoc w R
capreomycin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.9 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288764 p.Thr160Pro missense_variant 0.11 pyrazinamide Assoc w R
pncA 2289081 p.Pro54Leu missense_variant 0.89 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol Assoc w R
ethA 4327081 c.392delG frameshift_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 576400 c.1053C>T synonymous_variant 0.91 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rpoB 761461 p.Arg552Leu missense_variant 0.9 rifampicin Uncertain significance
rpoC 766645 p.Glu1092Asp missense_variant 0.13 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 776100 p.Thr794Ile missense_variant 0.13 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.12 clofazimine
bedaquiline
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
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102295 p.Thr250Ala missense_variant 0.12 ethionamide Uncertain significance
delamanid
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.11 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.14 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
Rv2477c 2783502 c.541T>C synonymous_variant 0.88 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2784443 c.-401G>T upstream_gene_variant 0.93 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 0.15 cycloserine
ald 3086987 p.Gln56His missense_variant 0.9 cycloserine
ald 3087367 p.Ala183Val missense_variant 0.92 cycloserine
ald 3087711 p.Val298Met missense_variant 0.94 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.12 pyrazinamide Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.12 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877536 c.972C>T synonymous_variant 0.9 rifampicin Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.12 ethambutol Not assoc w R
ubiA 4269124 p.Ala237Val missense_variant 0.93 ethambutol Uncertain significance
whiB6 4338307 p.Ala72Gly missense_variant 0.9 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 0.11 capreomycin
amikacin
kanamycin