TB-Profiler result

Run: ERR4798336
Summary

Run ID: ERR4798336

Sample name:

Date: 2024-04-15T06:53:04.354927

Number of reads: 3388398

Percentage reads mapped: 99.4

Median coverage: 97.0

Strain: lineage1.2.2.2;lineage3

Spoligotype:

Drug-resistance: Pre-XDR-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 0.45
lineage1.2.2 Indo-Oceanic RD239 0.53
lineage1.2.2.2 Indo-Oceanic RD239 0.52
lineage1 Indo-Oceanic RD239 0.53
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr Assoc w R
p.Ser450Leu Assoc w R
isoniazid inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Leu Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Ala143Pro Mutation from literature
streptomycin
fluoroquinolones
moxifloxacin gyrB p.Thr500Asn Uncertain significance Mutation from literature
gyrA p.Ser91Pro Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Thr500Asn Uncertain significance Mutation from literature
gyrA p.Ser91Pro Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T
ethA p.Pro378Leu 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
gyrB 6738 p.Thr500Asn missense_variant 0.58 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
gyrA 7572 p.Ser91Pro missense_variant 0.5 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761109 p.Asp435Tyr missense_variant 0.71 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.28 rifampicin Assoc w R
inhA 1673423 c.-779G>T upstream_gene_variant 0.49 ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
isoniazid Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288815 p.Ala143Pro missense_variant 0.47 pyrazinamide Mutation from literature
embB 4247429 p.Met306Leu missense_variant 0.49 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.49 ethambutol Assoc w R
ethA 4326341 p.Pro378Leu missense_variant 0.48 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
gyrB 5075 c.-165C>T upstream_gene_variant 0.47 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.51 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.5 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8452 p.Ala384Val missense_variant 0.45 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.44 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 13298 p.Ile87Met missense_variant 0.44 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.47 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.47 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.52 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.38 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.5 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.44 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.54 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.47 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.47 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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.59 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.54 ethambutol Not assoc w R
embR 1417040 p.Leu103Pro missense_variant 0.46 ethambutol Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.57 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.55 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473021 n.1176G>A non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.45 linezolid Not assoc w R
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
tlyA 1918719 c.780G>A synonymous_variant 0.37 capreomycin
bacA 2062922 p.Ile603Val missense_variant 0.59 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2064372 c.357A>G synonymous_variant 0.42 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ndh 2102240 p.Arg268His missense_variant 0.51 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.6 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.44 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.61 clofazimine Not assoc w R
bedaquiline Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.54 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.52 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.47 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.63 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.45 isoniazid Not assoc w R
ahpC 2726418 p.Glu76Lys missense_variant 0.53 isoniazid Uncertain significance
Rv2477c 2782498 c.1545C>T synonymous_variant 0.44 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.48 ethionamide Uncertain significance
Rv3236c 3612109 p.Phe336Leu missense_variant 0.53 pyrazinamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.54 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.51 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.5 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.57 pyrazinamide Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.41 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.47 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4138622 c.1134C>T synonymous_variant 0.41 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 4240671 p.Thr270Ile missense_variant 0.49 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.51 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.44 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243228 c.-5G>A upstream_gene_variant 0.44 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.54 ethambutol Not assoc w R
embB 4246430 c.-84C>T upstream_gene_variant 0.52 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.52 ethambutol Not assoc w R
aftB 4267960 p.Val293Met missense_variant 0.53 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.55 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.56 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.53 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.52 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.59 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin 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 4338603 c.-82C>T upstream_gene_variant 0.54 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407848 p.Ala119Thr missense_variant 0.48 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.5 streptomycin Not assoc w R
gid 4408060 p.His48Pro missense_variant 0.48 streptomycin Uncertain significance
gid 4408072 p.Leu44Pro missense_variant 0.53 streptomycin Uncertain significance