TB-Profiler result

Run: SRR20969695
Summary

Run ID: SRR20969695

Sample name:

Date: 2024-04-15T22:38:42.300458

Number of reads: 9437558

Percentage reads mapped: 99.64

Median coverage: 257.0

Strain: lineage2.2.1;lineage4.5

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.16
lineage2 East-Asian RD105 0.84
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.85
lineage2.2 East-Asian (Beijing) RD105;RD207 0.84
lineage4 Euro-American None 0.14
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.-777C>T Assoc w R Alias fabG1_c.-15C>T. 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
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 1673425 c.-777C>T upstream_gene_variant 0.13 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.84 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.86 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.84 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.15 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.85 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.84 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.82 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.86 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 0.87 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.86 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.85 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.83 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.83 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.86 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475866 n.2209T>C non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rpsA 1834177 c.636A>C synonymous_variant 0.85 pyrazinamide Not assoc w R - Interim
rpsA 1834643 p.Asp368Asn missense_variant 0.84 pyrazinamide Uncertain significance
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
katG 2154724 p.Arg463Leu missense_variant 0.81 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.87 pyrazinamide Not assoc w R
PPE35 2170568 p.Ile15Met 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
ald 3086788 c.-32T>C upstream_gene_variant 0.83 cycloserine
ald 3087448 p.Glu210Ala missense_variant 0.84 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.86 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.79 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877750 p.Asp253Gly missense_variant 0.17 rifampicin Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 0.22 rifampicin Not assoc w R
rpoA 3879070 c.-563G>A upstream_gene_variant 0.12 rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 0.17 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.85 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.79 ethambutol Not assoc w R
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 4407588 c.615A>G synonymous_variant 0.86 streptomycin Not assoc w R
gid 4407693 p.Glu170Asp missense_variant 0.84 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.82 streptomycin Not assoc w R