TB-Profiler result

Run: ERR067701
Summary

Run ID: ERR067701

Sample name:

Date: 2024-04-16T11:52:10.364820

Number of reads: 2946534

Percentage reads mapped: 99.56

Median coverage: 66.0

Strain: lineage2.2.1;lineage4.1.2.1

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 0.76
lineage4.1 Euro-American None 0.27
lineage4.1.2 Euro-American None 0.26
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.26
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.77
lineage2.2 East-Asian (Beijing) RD105;RD207 0.76
lineage4 Euro-American None 0.28
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Gly406Ala Assoc w R
pyrazinamide pncA p.Trp68Gly Assoc w R
streptomycin rpsL p.Lys43Arg 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)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
c.-12C>T Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.26 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
katG 2155167 p.Ser315Thr missense_variant 0.23 isoniazid Assoc w R High-level resistance
pncA 2289040 p.Trp68Gly missense_variant 0.2 pyrazinamide Assoc w R
eis 2715342 c.-10G>A upstream_gene_variant 0.86 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
eis 2715344 c.-12C>T upstream_gene_variant 0.15 kanamycin Assoc w R
embB 4247429 p.Met306Val missense_variant 0.24 ethambutol Assoc w R
embB 4247730 p.Gly406Ala missense_variant 0.83 ethambutol 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
dnaA 698 p.Arg233Gln missense_variant 0.24 isoniazid Uncertain significance
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 491591 p.Lys270Met missense_variant 0.24 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.83 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575679 p.Asn111Ser missense_variant 0.31 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.77 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.84 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.66 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.75 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.21 ethionamide Uncertain significance
rpoB 760106 c.300G>A synonymous_variant 0.16 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.14 rifampicin Not assoc w R
rpoB 761292 p.Val496Leu missense_variant 0.31 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.82 rifampicin Not assoc w R
rpoC 764703 p.Lys445Arg missense_variant 0.74 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.42 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 0.75 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.8 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.73 clofazimine
bedaquiline
rpsL 781276 c.-284A>C upstream_gene_variant 0.34 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.75 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254583 c.-49A>C upstream_gene_variant 0.26 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.87 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.84 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 0.74 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.81 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
kasA 2518076 c.-39C>T upstream_gene_variant 0.24 isoniazid
ald 3086731 c.-89A>G upstream_gene_variant 0.76 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.81 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 0.76 bedaquiline Uncertain significance
rifampicin Not assoc w R
glpK 4139881 c.-126T>C upstream_gene_variant 0.28 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4239298 c.-565C>T upstream_gene_variant 0.25 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 0.22 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.78 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.76 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.77 ethambutol Not assoc w R
ethA 4327298 p.Met59Arg missense_variant 0.24 ethionamide Uncertain significance
whiB6 4338371 p.Thr51Pro missense_variant 0.78 capreomycin Not assoc w R
amikacin Not assoc w R
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 4407588 c.615A>G synonymous_variant 0.73 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.81 streptomycin Not assoc w R