TB-Profiler result

Run: ERR751349
Summary

Run ID: ERR751349

Sample name:

Date: 2025-05-07T06:20:09.799252

Number of reads: 4775407

Percentage reads mapped: 99.59

Median coverage: 102.0

Strain: lineage4.8;lineage5.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 0.73
lineage4.8 Euro-American (mainly T) RD219 0.68
lineage5.1.1 West-Africa 1 RD711 0.3
lineage5 West-Africa 1 RD711 0.33
lineage5.1 West-Africa 1 RD711 0.29
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 6446 p.Ala403Ser missense_variant 0.44 levofloxacin Not assoc w R
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 0.32 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.31 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.25 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9566 c.2265C>T synonymous_variant 0.29 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13579 c.-21G>A upstream_gene_variant 0.35 isoniazid Uncertain significance
Rv0010c 13826 c.-268G>A upstream_gene_variant 0.66 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.38 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.65 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.29 ethionamide Uncertain significance
hadA 731750 c.-180G>C upstream_gene_variant 0.29 isoniazid Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.67 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.27 rifampicin Not assoc w R
rpoB 763280 c.3474C>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.21 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
Rv1129c 1253330 p.Gly402Glu missense_variant 0.76 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.23 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.24 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv1258c 1407273 p.Asp23Val missense_variant 0.25 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.26 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 1673338 c.-864G>A upstream_gene_variant 0.32 ethionamide Uncertain significance
isoniazid Uncertain significance
tsnR 1853565 c.-41G>A upstream_gene_variant 0.31 linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.35 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 0.35 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
streptomycin Not assoc w R
ndh 2101840 c.1203G>A synonymous_variant 0.29 delamanid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ndh 2101921 c.1122G>A synonymous_variant 0.29 delamanid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ndh 2103112 c.-70G>T upstream_gene_variant 0.27 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.28 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.28 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.68 pyrazinamide Not assoc w R
Rv1979c 2222569 p.Ala199Val missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2290062 c.-821G>A upstream_gene_variant 0.29 pyrazinamide Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.31 isoniazid Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.67 capreomycin Uncertain significance
ald 3087084 c.266delA frameshift_variant 0.27 cycloserine Uncertain significance
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 0.25 cycloserine Uncertain significance
Rv3083 3449644 p.Ala381Thr missense_variant 1.0 ethionamide Uncertain significance
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.67 pyrazinamide Not assoc w R
lpqB 3624350 c.561G>T synonymous_variant 0.21 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.27 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.31 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840932 c.489C>T synonymous_variant 0.38 cycloserine Uncertain significance
rpoA 3878493 c.15G>A synonymous_variant 0.3 rifampicin Not assoc w R - Interim
ddn 3986987 c.144G>T synonymous_variant 0.3 delamanid Not assoc w R - Interim
pretomanid Uncertain significance
ddn 3987180 p.Asp113Asn missense_variant 0.33 delamanid Uncertain significance
pretomanid Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 0.77 pyrazinamide Not assoc w R
clpC1 4040824 c.-120C>T upstream_gene_variant 0.39 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.28 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 4139131 p.Glu209Lys missense_variant 0.32 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Not assoc w R
streptomycin Uncertain significance
embC 4239843 c.-20A>C upstream_gene_variant 0.25 ethambutol Not assoc w R - Interim
embC 4240671 p.Thr270Ile missense_variant 0.24 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.26 ethambutol Not assoc w R
embA 4244635 p.Val468Ala missense_variant 0.35 ethambutol Not assoc w R - Interim
embA 4245147 p.Pro639Ser missense_variant 0.34 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.28 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.28 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.3 ethambutol Not assoc w R
aftB 4269768 c.-932C>A upstream_gene_variant 0.22 ethambutol Uncertain significance
ethA 4326928 c.546C>T synonymous_variant 0.32 ethionamide Not assoc w R - Interim
ethA 4327103 p.Gly124Asp missense_variant 0.35 ethionamide Uncertain significance
whiB6 4338547 c.-26A>G upstream_gene_variant 0.22 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 0.3 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 0.34 streptomycin Not assoc w R