TB-Profiler result

Run: ERR2516067
Summary

Run ID: ERR2516067

Sample name:

Date: 2025-05-17T12:07:40.516903

Number of reads: 1050463

Percentage reads mapped: 99.62

Median coverage: 57.0

Strain: lineage1.2.2.2;lineage4.1.2

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.16
lineage1.2.2.2 Indo-Oceanic RD239 0.12
lineage4.1 Euro-American None 0.83
lineage4.1.2 Euro-American None 0.82
lineage4 Euro-American None 0.9
lineage1 Indo-Oceanic RD239 0.15
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid
ethambutol embB p.Met306Val Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 0.15 rifampicin Assoc w R
embB 4247429 p.Met306Val missense_variant 0.23 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
gyrB 5075 c.-165C>T upstream_gene_variant 0.29 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 7879 p.Asn193Ser missense_variant 0.15 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8452 p.Ala384Val missense_variant 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.18 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 13460 c.99T>C synonymous_variant 0.24 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.27 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.29 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.22 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.81 ethionamide Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.2 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.13 rifampicin Not assoc w R
rpoC 763552 c.183C>T synonymous_variant 0.25 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.34 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.35 rifampicin Not assoc w R
rpoC 764333 p.Pro322Ser missense_variant 0.21 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.84 rifampicin Not assoc w R
rpoC 767123 p.Val1252Leu missense_variant 0.19 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 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 0.11 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
embR 1417019 p.Cys110Tyr missense_variant 0.22 ethambutol Not assoc w R
embR 1417140 p.Ala70Ser missense_variant 0.84 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.19 ethambutol Uncertain significance
embR 1418018 c.-671C>T upstream_gene_variant 0.89 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
inhA 1673249 c.-953C>T upstream_gene_variant 0.82 ethionamide Uncertain significance
isoniazid 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 0.17 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 0.13 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.2 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.24 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.25 bedaquiline Uncertain significance
clofazimine Not assoc w R
kasA 2518132 non_coding_transcript_variant 0.22 isoniazid Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.18 isoniazid Uncertain significance
folC 2747022 p.Val193Ile missense_variant 0.83 para-aminosalicylic_acid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3083 3448714 p.Asp71His missense_variant 0.17 ethionamide Uncertain significance
Rv3083 3448894 p.Tyr131Asp missense_variant 0.91 ethionamide Uncertain significance
Rv3083 3449642 p.Asn380Ser missense_variant 0.93 ethionamide Uncertain significance
whiB7 3568921 c.-242G>C upstream_gene_variant 0.9 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.15 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 0.39 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
fbiA 3641164 p.Ile208Val missense_variant 0.96 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.2 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.12 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 0.18 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.14 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 0.84 ethambutol Not assoc w R
embB 4246979 p.Gly156Cys missense_variant 0.29 ethambutol Not assoc w R - Interim
aftB 4268861 c.-25T>C upstream_gene_variant 0.8 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.24 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.18 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.14 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.18 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.15 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
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 0.26 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 0.28 streptomycin Not assoc w R
gid 4407848 p.Ala119Thr missense_variant 0.13 streptomycin Uncertain significance