TB-Profiler result

Run: ERR234566
Summary

Run ID: ERR234566

Sample name:

Date: 2024-10-04T05:09:27.432168

Number of reads: 3185813

Percentage reads mapped: 99.62

Median coverage: 69.0

Strain: lineage2.2.1;lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.49
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.44
lineage2.2 East-Asian (Beijing) RD105;RD207 0.49
lineage4 Euro-American None 0.52
lineage4.8 Euro-American (mainly T) RD219 0.49
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.Asn296His Uncertain significance Mutation from literature
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Thr47Ala Assoc w R
p.Val7Gly Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide ethA p.Trp256* Assoc w R
c.110delA 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
rpoB 761155 p.Ser450Leu missense_variant 0.23 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.96 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.96 isoniazid Assoc w R High-level resistance
pncA 2289103 p.Thr47Ala missense_variant 0.37 pyrazinamide Assoc w R
pncA 2289222 p.Val7Gly missense_variant 0.18 pyrazinamide Assoc w R
eis 2715342 c.-10G>A upstream_gene_variant 0.24 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
embB 4247399 p.Asn296His missense_variant 0.25 ethambutol Uncertain significance Mutation from literature
embB 4248003 p.Gln497Arg missense_variant 0.18 ethambutol Assoc w R
ethA 4326707 p.Trp256* stop_gained 0.14 ethionamide Assoc w R
ethA 4327363 c.110delA frameshift_variant 0.3 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 0.59 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.48 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.3 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.56 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.36 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.49 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.52 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.53 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.52 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 0.53 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.57 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 778107 p.Ser125Cys missense_variant 0.39 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.45 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
sigE 1364202 c.-211G>A upstream_gene_variant 0.47 pyrazinamide
Rv1258c 1406760 c.580_581insC frameshift_variant 0.54 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.51 capreomycin Not assoc w R
linezolid Not assoc w R
inhA 1673406 c.-796C>T upstream_gene_variant 0.24 isoniazid Uncertain significance
ethionamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.4 pyrazinamide Not assoc w R - Interim
rpsA 1834427 p.Ile296Phe missense_variant 0.2 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 0.57 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 0.54 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.32 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser 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
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.46 capreomycin
Rv2680 2995927 c.-178T>C upstream_gene_variant 0.3 capreomycin
ald 3086731 c.-89A>G upstream_gene_variant 0.44 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.42 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.54 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.51 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.48 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877949 p.Thr187Ala missense_variant 0.23 rifampicin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.35 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.39 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.41 ethambutol Not assoc w R
ubiA 4269298 p.Ile179Thr missense_variant 0.17 ethambutol Uncertain significance
ethA 4328378 c.-905G>C upstream_gene_variant 0.59 ethionamide
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 0.48 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.53 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.44 streptomycin Not assoc w R