TB-Profiler result

Run: ERR161122
Summary

Run ID: ERR161122

Sample name:

Date: 2025-05-27T09:30:45.035224

Number of reads: 3660461

Percentage reads mapped: 99.36

Median coverage: 80.0

Strain: lineage1.2.2.1;lineage4.3.4.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2.1 Indo-Oceanic RD239 0.92
lineage4.3 Euro-American (LAM) None 0.06
lineage1.2.2 Indo-Oceanic RD239 0.94
lineage4 Euro-American None 0.06
lineage1 Indo-Oceanic RD239 0.93
lineage4.3.4.2 Euro-American (LAM) RD174 0.06
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
dnaA 237 c.237G>A synonymous_variant 0.87 isoniazid Not assoc w R - Interim
gyrB 5075 c.-165C>T upstream_gene_variant 0.91 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.92 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 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.91 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 0.94 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.94 isoniazid Not assoc w R
fgd1 491060 p.Met93Thr missense_variant 0.9 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.94 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
ccsA 620252 p.Gly121Glu missense_variant 0.83 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
ccsA 620659 p.Arg257Cys missense_variant 0.97 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.9 ethionamide Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.94 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.94 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.85 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.86 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 0.92 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.91 linezolid Not assoc w R
rplC 800799 c.-10G>A upstream_gene_variant 0.87 linezolid Uncertain significance
rplC 800899 p.Ala31Thr missense_variant 0.93 linezolid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.81 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.93 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.93 ethambutol Uncertain significance
embR 1417793 c.-446C>T upstream_gene_variant 0.98 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1471842 n.-4T>G upstream_gene_variant 0.91 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
tsnR 1853972 p.Gly123Ser missense_variant 0.88 linezolid Uncertain significance
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
bacA 2062922 p.Ile603Val missense_variant 0.88 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
streptomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.92 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.93 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.88 bedaquiline Not assoc w R - Interim
clofazimine 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
pncA 2289346 c.-105A>G upstream_gene_variant 0.89 pyrazinamide Uncertain significance
kasA 2518132 non_coding_transcript_variant 0.91 isoniazid Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.9 isoniazid Uncertain significance
Rv2752c 3067032 c.-841C>G upstream_gene_variant 0.85 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
ald 3086739 c.-81G>A upstream_gene_variant 0.83 cycloserine Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3083 3448714 p.Asp71His missense_variant 0.91 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.96 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.97 pyrazinamide Not assoc w R - Interim
panD 4044313 c.-32C>T upstream_gene_variant 0.84 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.91 ethambutol Not assoc w R
isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
streptomycin Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.92 ethambutol Not assoc w R
embC 4240750 c.888C>T synonymous_variant 0.93 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.94 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.94 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.91 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.91 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.91 ethambutol Not assoc w R
ethA 4326439 p.Asn345Lys missense_variant 0.95 ethionamide Uncertain significance
ethA 4327450 c.24C>T synonymous_variant 0.94 ethionamide Not assoc w R - Interim
whiB6 4338310 p.Gly71Asp missense_variant 0.91 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.98 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 0.9 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.83 streptomycin Not assoc w R