TB-Profiler result

Run: SRR6485149
Summary

Run ID: SRR6485149

Sample name:

Date: 2024-04-15T15:19:37.795420

Number of reads: 3882898

Percentage reads mapped: 99.44

Median coverage: 84.0

Strain: lineage2.2.1;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 0.68
lineage2 East-Asian RD105 0.32
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.3
lineage2.2 East-Asian (Beijing) RD105;RD207 0.35
lineage4 Euro-American None 0.65
lineage4.3.3 Euro-American (LAM) RD115 0.68
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 rpsL p.Lys43Arg Assoc w R
gid c.336_359dupTGAGATCGTGCGGGGGCGCGCCGA Mutation from literature
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
rpsL 781687 p.Lys43Arg missense_variant 0.28 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.31 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
gid 4407843 c.336_359dupTGAGATCGTGCGGGGGCGCGCCGA disruptive_inframe_insertion 0.5 streptomycin Mutation from literature
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 0.76 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9209 p.Lys636Asn missense_variant 0.65 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 0.31 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.3 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.38 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.44 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.33 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.45 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.74 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.4 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 0.35 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.34 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.31 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 0.33 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.36 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.25 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11 ethionamide
isoniazid
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11 ethionamide
isoniazid
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31 ethionamide
isoniazid
rpsA 1834177 c.636A>C synonymous_variant 0.32 pyrazinamide Not assoc w R - Interim
rpsA 1834836 p.Met432Thr missense_variant 0.75 pyrazinamide Not assoc w R - Interim
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 0.24 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.72 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.31 pyrazinamide Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.17 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.18 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.73 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.61 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.7 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.31 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 0.38 bedaquiline Uncertain significance
rifampicin Not assoc w R
ddn 3987242 c.399T>C synonymous_variant 0.35 delamanid
pretomanid
clpC1 4038287 c.2418C>T synonymous_variant 0.67 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.54 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.29 ethambutol Not assoc w R
embB 4246555 c.42G>C synonymous_variant 0.38 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.38 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.32 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.26 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.21 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 0.26 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.18 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.7 streptomycin Not assoc w R