TB-Profiler result

Run: ERR13265708
Summary

Run ID: ERR13265708

Sample name:

Date: 2025-02-11T13:56:18.808253

Number of reads: 5092320

Percentage reads mapped: 98.62

Median coverage: 154.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
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
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 7412 c.111C>G synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 7433 c.132G>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 7442 c.141G>T synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 7457 c.156T>C synonymous_variant 0.1 levofloxacin
moxifloxacin
gyrA 7469 c.168C>G synonymous_variant 0.11 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7511 c.210C>T synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 7514 c.213C>G synonymous_variant 0.11 levofloxacin
moxifloxacin
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 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.99 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801021 c.213C>T synonymous_variant 1.0 linezolid Not assoc w R - Interim
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
sigE 1364958 c.546G>T synonymous_variant 1.0 pyrazinamide
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674542 p.Ala114Glu missense_variant 0.13 isoniazid
ethionamide
inhA 1674546 c.345T>C synonymous_variant 0.13 isoniazid
ethionamide
inhA 1674550 p.Ser117Ala missense_variant 0.13 isoniazid
ethionamide
inhA 1674570 c.369G>C synonymous_variant 0.15 isoniazid
ethionamide
inhA 1674573 c.372G>A synonymous_variant 0.15 isoniazid
ethionamide
inhA 1674576 c.375T>C synonymous_variant 0.14 isoniazid
ethionamide
inhA 1674579 c.378G>C synonymous_variant 0.14 isoniazid
ethionamide
inhA 1674585 c.384T>C synonymous_variant 0.15 isoniazid
ethionamide
inhA 1674589 p.Met130Leu missense_variant 0.16 isoniazid
ethionamide
inhA 1674600 c.399G>C synonymous_variant 0.16 isoniazid
ethionamide
inhA 1674601 p.Leu134Val missense_variant 0.16 isoniazid
ethionamide
inhA 1674624 c.423A>C synonymous_variant 0.15 isoniazid
ethionamide
inhA 1674627 c.426T>G synonymous_variant 0.15 isoniazid
ethionamide
inhA 1674639 c.438C>T synonymous_variant 0.14 isoniazid
ethionamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 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 0.99 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 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 2517917 c.-198G>T upstream_gene_variant 0.16 isoniazid
kasA 2517926 c.-189G>A upstream_gene_variant 0.15 isoniazid
kasA 2517941 c.-174C>G upstream_gene_variant 0.13 isoniazid
kasA 2518564 c.450C>G synonymous_variant 0.13 isoniazid
kasA 2518567 c.453G>C synonymous_variant 0.13 isoniazid
kasA 2518570 c.456G>C synonymous_variant 0.12 isoniazid
kasA 2518574 p.Ile154Val missense_variant 0.12 isoniazid
kasA 2518579 c.465T>C synonymous_variant 0.12 isoniazid
kasA 2518588 c.474T>C synonymous_variant 0.12 isoniazid
kasA 2518591 c.477G>C synonymous_variant 0.12 isoniazid
kasA 2518594 c.480C>T synonymous_variant 0.12 isoniazid
kasA 2518606 c.492G>C synonymous_variant 0.12 isoniazid
kasA 2518609 p.Met165Ile missense_variant 0.13 isoniazid
kasA 2518618 c.504G>C synonymous_variant 0.14 isoniazid
kasA 2518624 c.510C>G synonymous_variant 0.14 isoniazid
kasA 2518636 c.522C>T synonymous_variant 0.15 isoniazid
kasA 2518642 c.528A>G synonymous_variant 0.15 isoniazid
kasA 2518672 c.558G>C synonymous_variant 0.13 isoniazid
kasA 2518684 c.570C>G synonymous_variant 0.1 isoniazid
Rv2681 2997797 c.1067_1068delCG frameshift_variant 1.0 capreomycin Uncertain significance
thyX 3067286 c.660C>T synonymous_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 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 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038971 c.1734T>C synonymous_variant 0.13 pyrazinamide
clpC1 4038974 c.1731T>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4038989 c.1716T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038997 c.1708T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4039001 p.Asn568Glu missense_variant 0.13 pyrazinamide
clpC1 4039004 c.1701C>G synonymous_variant 0.13 pyrazinamide
clpC1 4039022 c.1683A>G synonymous_variant 0.14 pyrazinamide
clpC1 4039034 c.1671C>G synonymous_variant 0.16 pyrazinamide
clpC1 4039046 c.1659C>T synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
clpC1 4039073 c.1632C>G synonymous_variant 0.18 pyrazinamide
clpC1 4039085 c.1620A>G synonymous_variant 0.17 pyrazinamide
clpC1 4039090 c.1615C>T synonymous_variant 0.19 pyrazinamide
clpC1 4039097 c.1608G>C synonymous_variant 0.2 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.19 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.18 pyrazinamide
clpC1 4039121 c.1584T>C synonymous_variant 0.2 pyrazinamide
clpC1 4039139 c.1566G>A synonymous_variant 0.18 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.18 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.19 pyrazinamide
clpC1 4039169 p.Glu512Asp missense_variant 0.18 pyrazinamide
clpC1 4039178 c.1527G>C synonymous_variant 0.17 pyrazinamide
clpC1 4039183 c.1522T>C synonymous_variant 0.16 pyrazinamide
glpK 4138861 p.Asn299Asp missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 1.0 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 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 1.0 streptomycin Not assoc w R