TB-Profiler result

Run: ERR2512780
Summary

Run ID: ERR2512780

Sample name:

Date: 2024-10-04T06:54:36.278742

Number of reads: 3003542

Percentage reads mapped: 99.44

Median coverage: 97.0

Strain: lineage2.2.1;lineage6.1.3

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.71
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.68
lineage2.2 East-Asian (Beijing) RD105;RD207 0.7
lineage6.1.3 West-Africa 2 RD702 0.34
lineage6 West-Africa 2 RD702 0.33
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 embC p.Ala307Thr Uncertain significance Mutation from literature
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
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
katG 2155168 p.Ser315Thr missense_variant 0.67 isoniazid Assoc w R High-level resistance
embC 4240781 p.Ala307Thr missense_variant 0.38 ethambutol Uncertain significance 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
gyrB 6446 p.Ala403Ser missense_variant 0.31 levofloxacin Not assoc w R
moxifloxacin 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 8493 p.Leu398Phe missense_variant 0.23 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8806 p.Asp502Gly missense_variant 0.3 levofloxacin
moxifloxacin
gyrA 9143 c.1842T>C synonymous_variant 0.36 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
Rv0010c 13460 c.99T>C synonymous_variant 0.25 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.28 isoniazid Not assoc w R
fgd1 491668 p.Lys296Glu missense_variant 0.29 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.64 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.65 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 656432 p.Gly347Ser missense_variant 0.23 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.7 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.68 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.28 ethionamide
rpoB 760855 p.Thr350Ile missense_variant 0.26 rifampicin Uncertain significance
rpoB 760969 p.Ser388Leu missense_variant 0.31 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.41 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766231 c.2862T>C synonymous_variant 0.28 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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.54 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.7 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800232 c.-577G>T upstream_gene_variant 0.31 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.4 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv1258c 1406253 p.Gly363Val missense_variant 0.66 streptomycin Not assoc w R
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1406685 p.Val219Ala missense_variant 0.3 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.7 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1416633 p.Leu239Val missense_variant 0.27 ethambutol Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.27 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.34 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472912 n.1067C>T non_coding_transcript_exon_variant 0.65 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473633 n.-25C>T upstream_gene_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674210 c.9A>C synonymous_variant 0.72 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
inhA 1674434 p.Val78Ala missense_variant 0.39 isoniazid Not assoc w R
ethionamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.67 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 2062922 p.Ile603Val missense_variant 0.24 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063121 c.1608A>T synonymous_variant 0.29 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.28 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.3 bedaquiline Not assoc w R - Interim
clofazimine 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
Rv1979c 2223685 c.-521G>A upstream_gene_variant 0.72 bedaquiline
clofazimine
kasA 2518132 c.18C>T synonymous_variant 0.35 isoniazid
folC 2747727 c.-129C>G upstream_gene_variant 0.69 para-aminosalicylic_acid
ald 3086728 c.-92C>T upstream_gene_variant 0.34 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 0.36 cycloserine
ald 3087412 p.Asp198Val missense_variant 0.27 cycloserine
Rv3236c 3612143 p.Arg325His missense_variant 0.26 pyrazinamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.76 pyrazinamide Not assoc w R - Interim
lpqB 3624350 c.561G>T synonymous_variant 0.28 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.29 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626184 p.Ala144Thr missense_variant 0.3 rifampicin
bedaquiline
mtrB 3626562 p.Pro18Ser missense_variant 0.62 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877740 c.768G>C synonymous_variant 0.31 rifampicin
glpK 4138377 p.Val460Ala missense_variant 0.34 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.36 ethambutol 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 0.68 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.32 ethambutol Not assoc w R
embA 4244379 p.Pro383Ser missense_variant 0.39 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.3 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.28 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.64 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.31 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.37 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 0.33 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.27 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 0.3 ethionamide Uncertain significance
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 4338602 c.-81A>C upstream_gene_variant 0.28 kanamycin
capreomycin
amikacin
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.66 streptomycin Not assoc w R
gid 4408034 p.Glu57Lys missense_variant 0.26 streptomycin Uncertain significance