TB-Profiler result

Run: ERR13275971
Summary

Run ID: ERR13275971

Sample name:

Date: 2025-02-11T12:22:55.019611

Number of reads: 3341095

Percentage reads mapped: 99.55

Median coverage: 102.0

Strain: lineage2.2.1;lineage4.2.2

Spoligotype:

Drug-resistance: HR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.56
lineage2 East-Asian RD105 0.43
lineage4.2 Euro-American None 0.6
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.42
lineage2.2 East-Asian (Beijing) RD105;RD207 0.45
lineage4 Euro-American None 0.6
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 0.43 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.47 isoniazid Assoc w R High-level resistance
pncA 2289222 p.Val7Gly missense_variant 0.46 pyrazinamide Assoc w R
ethA 4326707 p.Trp256* stop_gained 0.39 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
fgd1 490961 p.Ala60Gly missense_variant 0.62 pretomanid
delamanid
clofazimine
fgd1 491742 c.960T>C synonymous_variant 0.39 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.38 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576077 c.730C>T synonymous_variant 0.56 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.48 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.4 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.37 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.49 rifampicin Not assoc w R
rpoC 764326 c.957G>C synonymous_variant 0.52 rifampicin Not assoc w R - Interim
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 0.44 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 0.46 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.57 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.45 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 0.37 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471648 n.-198A>C upstream_gene_variant 0.49 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.47 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
bacA 2063685 c.1044G>A synonymous_variant 0.51 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.5 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.33 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.44 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
eis 2715213 c.120G>T synonymous_variant 0.56 kanamycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.57 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086731 c.-89A>G upstream_gene_variant 0.45 cycloserine
ald 3086742 c.-78A>C upstream_gene_variant 0.55 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612012 p.Leu369Val missense_variant 0.48 pyrazinamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.4 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 0.34 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4239334 c.-529T>C upstream_gene_variant 0.64 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.4 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.36 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.45 ethambutol Not assoc w R
whiB6 4338371 p.Thr51Pro missense_variant 0.4 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 0.42 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.46 streptomycin Not assoc w R