TB-Profiler result

Run: ERR161071
Summary

Run ID: ERR161071

Sample name:

Date: 2025-05-27T08:36:07.322793

Number of reads: 7187848

Percentage reads mapped: 99.4

Median coverage: 158.0

Strain: La1.1;lineage3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.86
La1.1 M.bovis None 0.14
La1 M.bovis None 0.14
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 467 p.His156Arg missense_variant 0.14 isoniazid 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 8285 c.984C>T synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8660 c.1359C>T synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_variant 0.13 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 13197 p.Thr121Ser missense_variant 0.17 isoniazid Not assoc w R
Rv0010c 13228 c.330delG frameshift_variant 0.18 isoniazid Uncertain significance
Rv0010c 13460 c.99T>C synonymous_variant 0.11 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.99 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.81 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.14 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.85 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.86 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766582 c.3213C>A synonymous_variant 0.89 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 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 778066 p.Ala139Thr missense_variant 0.14 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781517 c.-43C>T upstream_gene_variant 0.13 streptomycin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.99 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254582 c.-48A>G upstream_gene_variant 0.14 isoniazid Not assoc w R
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.19 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.19 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 1472437 n.592T>G non_coding_transcript_exon_variant 0.12 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1476704 n.3053dupC non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673254 c.-948A>C upstream_gene_variant 0.1 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1834859 p.Ala440Thr missense_variant 0.14 pyrazinamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.99 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.21 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
streptomycin Not assoc w R
ndh 2103173 c.-132delG upstream_gene_variant 0.13 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.99 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.14 isoniazid Not assoc w R
katG 2156025 c.87C>A synonymous_variant 0.14 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.99 pyrazinamide Not assoc w R
PPE35 2168011 p.Ser868Arg missense_variant 0.15 pyrazinamide Uncertain significance
PPE35 2168814 c.1798dupA frameshift_variant 0.13 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.13 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 2289047 c.195C>T synonymous_variant 0.81 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.88 pyrazinamide Uncertain significance
kasA 2518132 non_coding_transcript_variant 0.15 isoniazid Uncertain significance
ahpC 2726105 c.-88G>A upstream_gene_variant 0.81 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.86 amikacin Not assoc w R
ethambutol Not assoc w R
kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
streptomycin Not assoc w R - Interim
Rv2477c 2782927 c.1116A>G synonymous_variant 0.13 amikacin Not assoc w R - Interim
ethambutol Not assoc w R
kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
rifampicin Not assoc w R
streptomycin Not assoc w R
Rv2680 2995899 c.-205delC upstream_gene_variant 0.2 capreomycin Uncertain significance
Rv2681 2997325 p.Ala196Val missense_variant 0.15 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
ald 3087084 c.266delA frameshift_variant 0.15 cycloserine Uncertain significance
Rv3083 3448783 p.Val94Ile missense_variant 0.15 ethionamide Uncertain significance
lpqB 3623730 p.Ser394Leu missense_variant 0.14 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624350 c.561G>T synonymous_variant 0.11 bedaquiline Not assoc w R - Interim
rifampicin 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
mtrA 3627711 c.-362C>A upstream_gene_variant 0.14 bedaquiline Uncertain significance
rifampicin Uncertain significance
alr 3841473 c.-125G>A upstream_gene_variant 0.87 cycloserine Uncertain significance
alr 3841559 c.-211C>T upstream_gene_variant 0.86 cycloserine Uncertain significance
rpoA 3878568 c.-61G>A upstream_gene_variant 0.15 rifampicin Uncertain significance
clpC1 4038596 non_coding_transcript_variant 0.12 pyrazinamide Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.89 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.13 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
glpK 4138622 c.1134C>T synonymous_variant 0.86 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 - Interim
embC 4240671 p.Thr270Ile missense_variant 0.17 ethambutol Not assoc w R
embC 4241975 p.Gln705Glu missense_variant 0.2 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.86 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242970 c.3108C>T synonymous_variant 0.18 ethambutol Not assoc w R
embB 4247270 p.Leu253Ile missense_variant 0.81 ethambutol Uncertain significance
embB 4247646 p.Glu378Ala missense_variant 0.18 ethambutol Not assoc w R
embB 4249251 p.Ala913Val missense_variant 0.86 ethambutol Uncertain significance
aftB 4267858 p.Ile327Val missense_variant 0.11 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.13 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.14 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.13 ethambutol Not assoc w R
whiB6 4338365 p.Cys53Arg missense_variant 0.82 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 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 1.0 streptomycin Not assoc w R