TB-Profiler result

Run: ERR163943
Summary

Run ID: ERR163943

Sample name:

Date: 2026-01-08T03:02:51.685017

Number of reads: 3388088

Percentage reads mapped: 99.63

Median coverage: 73.0

Strain: lineage1.1;lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1 Indo-Oceanic RD239 12.42
lineage4 Euro-American None 87.71
lineage4.3 Euro-American (LAM) None 77.15
lineage4.3.4 Euro-American (LAM) RD174 78.69
lineage4.3.4.2 Euro-American (LAM) RD174 81.13
lineage4.3.4.2.1 Euro-American (LAM) RD174 81.12
lineage4.4.1.1 Euro-American None 5.26
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
gyrB 6112 p.Met291Ile missense_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.11 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6140 p.Val301Leu missense_variant 0.79 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 9143 c.1842T>C synonymous_variant 0.11 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 0.13 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.12 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
mshA 576000 p.Asp218Ala missense_variant 0.12 ethionamide Uncertain significance
isoniazid Not assoc w R - Interim
nusG 734116 c.-138T>C upstream_gene_variant 0.18 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.13 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.11 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.81 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.14 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 776395 p.Phe696Leu missense_variant 0.12 bedaquiline Uncertain significance
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 0.12 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.16 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
fbiC 1304757 c.1827A>G synonymous_variant 0.66 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin 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
PPE35 2167926 p.Leu896Ser missense_variant 0.12 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
pncA 2288724 p.Glu173Gly missense_variant 0.75 pyrazinamide Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.13 isoniazid Uncertain significance
Rv2681 2996912 c.174C>T synonymous_variant 0.19 capreomycin Not assoc w R
Rv2752c 3065305 p.Ala296Val missense_variant 0.12 ethambutol Not assoc w R
isoniazid Not assoc w R - Interim
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.78 para-aminosalicylic_acid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3083 3448714 p.Asp71His missense_variant 0.12 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.78 pyrazinamide Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.16 pyrazinamide 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 0.11 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
alr 3840719 c.630A>G synonymous_variant 0.69 cycloserine Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.73 pyrazinamide Not assoc w R
panD 4044740 c.-459C>T upstream_gene_variant 0.15 pyrazinamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.13 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.21 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.17 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.1 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.13 ethambutol Not assoc w R
ethA 4326682 p.Phe264Leu missense_variant 0.18 ethionamide 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 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 0.18 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.81 streptomycin Not assoc w R