TB-Profiler result

Run: ERR10112416
Summary

Run ID: ERR10112416

Sample name:

Date: 2024-10-05T02:39:00.083942

Number of reads: 1523166

Percentage reads mapped: 99.03

Median coverage: 41.0

Strain: lineage2.2.1.1

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 0.99
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 0.88
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.79
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.Trp39* Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethR p.Phe110Leu Uncertain significance Mutation from literature
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 2155996 p.Trp39* stop_gained 0.38 isoniazid Assoc w R High-level resistance
ethR 4327878 p.Phe110Leu missense_variant 0.53 ethionamide 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
gyrA 7362 p.Glu21Gln missense_variant 0.99 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
Rv0010c 13228 c.329_330dupGG frameshift_variant 0.29 isoniazid 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 1.0 isoniazid Not assoc w R
ethionamide 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 1.0 ethionamide Uncertain significance
rpoB 759782 c.-25G>A upstream_gene_variant 0.12 rifampicin
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
mmpL5 776182 p.Asp767Asn missense_variant 1.0 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 776258 c.2223C>A synonymous_variant 0.43 bedaquiline
clofazimine
mmpL5 777165 p.Ser439Tyr missense_variant 0.5 bedaquiline
clofazimine
mmpL5 777842 c.639C>T synonymous_variant 0.23 bedaquiline
clofazimine
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
rpsL 781301 c.-259C>T upstream_gene_variant 1.0 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781784 p.Gln75His missense_variant 0.31 streptomycin
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 1364247 c.-166C>T upstream_gene_variant 0.37 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 1476561 n.2904C>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1476704 n.3053dupC non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
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
ndh 2102524 p.Phe173Leu missense_variant 0.48 isoniazid
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2156534 c.-423G>A upstream_gene_variant 0.2 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170073 c.540C>T synonymous_variant 0.48 pyrazinamide
PPE35 2170917 c.-305C>A upstream_gene_variant 0.82 pyrazinamide
eis 2714846 p.Val163Ile missense_variant 1.0 kanamycin Not assoc w R
amikacin Not assoc w R
folC 2747543 p.Pro19Leu missense_variant 0.62 para-aminosalicylic_acid
pepQ 2860307 p.Gly38Arg missense_variant 0.18 bedaquiline
clofazimine
Rv2681 2997211 p.Gly158Val missense_variant 0.32 capreomycin
Rv2752c 3064647 c.1545G>T synonymous_variant 0.26 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyA 3074104 p.Pro123His missense_variant 0.16 para-aminosalicylic_acid
Rv3236c 3612287 p.Gly277Val missense_variant 0.15 pyrazinamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.99 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3625675 c.-765G>A upstream_gene_variant 0.19 rifampicin
bedaquiline
mtrB 3626562 p.Pro18Ser missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640395 c.-148T>C upstream_gene_variant 0.2 pretomanid
delamanid
clofazimine
fbiB 3640758 c.-777G>A upstream_gene_variant 0.22 pretomanid
delamanid
clofazimine
fbiA 3641199 p.Ser219Arg missense_variant 0.14 pretomanid
delamanid
clofazimine
fbiB 3642665 c.1131C>A synonymous_variant 0.23 pretomanid
delamanid
clofazimine
clpC1 4040016 c.688delG frameshift_variant 0.76 pyrazinamide
panD 4044842 c.-561G>T upstream_gene_variant 0.36 pyrazinamide
glpK 4139183 c.572dupG frameshift_variant 0.17 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
embA 4246071 p.Asn947Tyr missense_variant 0.16 ethambutol
embB 4247230 c.717G>T synonymous_variant 0.25 ethambutol
embB 4248115 c.1602C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
aftB 4268886 c.-51_-50insC upstream_gene_variant 0.11 ethambutol
aftB 4269378 c.-542C>A upstream_gene_variant 0.14 ethambutol
ethA 4326198 p.Val426Ile missense_variant 0.23 ethionamide
ethA 4327191 p.Asp95Tyr missense_variant 0.73 ethionamide
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