TB-Profiler result

Run: ERR4798955
Summary

Run ID: ERR4798955

Sample name:

Date: 2024-04-15T01:59:26.251244

Number of reads: 3944353

Percentage reads mapped: 99.6

Median coverage: 111.0

Strain: lineage2.2.1.1;lineage3;lineage4.1.2.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.14
lineage2 East-Asian RD105 0.2
lineage4.1 Euro-American None 0.62
lineage4.1.2 Euro-American None 0.61
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.65
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.17
lineage2.2 East-Asian (Beijing) RD105;RD207 0.2
lineage4 Euro-American None 0.67
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.12
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 embB p.Met306Val Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.12 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpsL 781687 p.Lys43Arg missense_variant 0.2 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.29 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.18 ethambutol 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 491591 p.Lys270Met missense_variant 0.67 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.39 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575679 p.Asn111Ser missense_variant 0.52 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.17 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.23 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.32 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.21 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.66 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.14 rifampicin Not assoc w R
rpoB 760061 c.255C>T synonymous_variant 0.63 rifampicin Not assoc w R - Interim
rpoB 760115 c.309C>T synonymous_variant 0.64 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.17 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.41 rifampicin Not assoc w R
rpoC 764363 p.Gly332Ser missense_variant 0.19 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.62 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.37 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.15 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.2 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.39 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302920 c.-11G>A upstream_gene_variant 0.74 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.18 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
fabG1 1673204 c.-236C>T upstream_gene_variant 0.16 ethionamide
isoniazid
rpsA 1834177 c.636A>C synonymous_variant 0.16 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 0.36 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.36 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2288755 p.Val163Met missense_variant 0.67 pyrazinamide Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.15 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.15 pyrazinamide
kasA 2518076 c.-39C>T upstream_gene_variant 0.58 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.15 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.15 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2477c 2783734 c.309C>T synonymous_variant 0.64 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.12 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.16 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.16 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.21 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3641490 c.-45G>A upstream_gene_variant 0.62 clofazimine
pretomanid
delamanid
rpoA 3878586 c.-79A>G upstream_gene_variant 0.32 rifampicin
panD 4044872 c.-591C>T upstream_gene_variant 0.18 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.19 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.66 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.12 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.6 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.19 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.23 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.99 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.32 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.16 streptomycin Not assoc w R