TB-Profiler result

Run: ERR137194
Summary

Run ID: ERR137194

Sample name:

Date: 2024-10-05T12:27:30.411174

Number of reads: 8978743

Percentage reads mapped: 99.65

Median coverage: 199.0

Strain: lineage2.2.1;lineage4.1.2.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.36
lineage4.1 Euro-American None 0.63
lineage4.1.2 Euro-American None 0.61
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.63
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.36
lineage2.2 East-Asian (Beijing) RD105;RD207 0.38
lineage4 Euro-American None 0.64
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.Val7Gly Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Trp256* 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
rpsL 781687 p.Lys43Arg missense_variant 0.31 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.33 isoniazid Assoc w R High-level resistance
pncA 2289222 p.Val7Gly missense_variant 0.41 pyrazinamide Assoc w R
ethA 4326707 p.Trp256* stop_gained 0.31 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 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
gyrA 9532 p.Gly744Ala missense_variant 0.62 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.67 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.37 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.65 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.41 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576328 c.981T>C synonymous_variant 0.6 isoniazid Not assoc w R - Interim
ethionamide
ccsA 620625 p.Ile245Met missense_variant 0.41 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.39 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.34 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.72 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.66 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.29 rifampicin Not assoc w R
rpoC 764617 c.1248C>T synonymous_variant 0.32 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 0.61 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.4 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.41 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.38 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.36 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.36 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1407079 c.261delC frameshift_variant 0.65 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.38 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 0.39 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.39 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.63 isoniazid
ahpC 2726327 c.135C>A synonymous_variant 0.61 isoniazid Not assoc w R - Interim
ald 3086731 c.-89A>G upstream_gene_variant 0.3 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449925 c.1422C>T synonymous_variant 0.64 ethionamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.37 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.37 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4041011 c.-307C>T upstream_gene_variant 0.61 pyrazinamide
embC 4239298 c.-565C>T upstream_gene_variant 0.58 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 0.66 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.37 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.36 ethambutol Not assoc w R
embA 4243969 p.Val246Gly missense_variant 0.61 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.32 ethambutol Not assoc w R
whiB6 4338371 p.Thr51Pro missense_variant 0.35 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.39 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.32 streptomycin Not assoc w R