TB-Profiler result

Run: ERR2513014
Summary

Run ID: ERR2513014

Sample name:

Date: 2024-03-26T15:46:22.714535

Number of reads: 3968798

Percentage reads mapped: 99.52

Median coverage: 131.0

Strain: lineage1.1.2;lineage4.1.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.21
lineage4.1 Euro-American None 0.76
lineage4.1.2 Euro-American None 0.78
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.8
lineage1.1 Indo-Oceanic RD239 0.23
lineage4 Euro-American None 0.77
lineage1 Indo-Oceanic RD239 0.22
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 pncA p.Phe106Leu Assoc w R - Interim
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
pncA 2288924 p.Phe106Leu missense_variant 0.24 pyrazinamide Assoc w R - Interim
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 0.23 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.22 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 0.24 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.25 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 0.2 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.23 isoniazid Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.74 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.19 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575679 p.Asn111Ser missense_variant 0.74 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.85 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.18 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.23 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.78 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.25 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.22 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.22 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.75 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.26 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.23 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 0.8 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.28 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.15 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.2 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.21 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.2 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
fabG1 1673283 c.-157A>C upstream_gene_variant 0.2 ethionamide
isoniazid
tsnR 1853974 c.369C>T synonymous_variant 0.27 linezolid Not assoc w R
tsnR 1853992 c.387C>T synonymous_variant 0.28 linezolid
tsnR 1854045 p.Tyr147Cys missense_variant 0.25 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917777 c.-163A>G upstream_gene_variant 0.17 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.23 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.19 isoniazid Not assoc w R
katG 2155557 c.555C>T synonymous_variant 0.22 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.2 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.2 pyrazinamide Uncertain significance
PPE35 2168963 c.1650A>G synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
PPE35 2169421 p.Asn398Tyr missense_variant 0.77 pyrazinamide Uncertain significance
Rv1979c 2221783 p.Ala461Glu missense_variant 0.24 clofazimine
bedaquiline Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.24 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.81 isoniazid
kasA 2518132 c.18C>T synonymous_variant 0.19 isoniazid
kasA 2519096 p.Val328Ile missense_variant 0.12 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.23 isoniazid
ahpC 2726672 c.480G>A synonymous_variant 0.25 isoniazid Not assoc w R - Interim
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.18 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.84 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.22 capreomycin
Rv2681 2996912 c.174C>T synonymous_variant 0.33 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.25 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.22 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.2 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624491 c.420G>A synonymous_variant 0.19 bedaquiline
rifampicin
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627199 p.Asp51Asn missense_variant 0.22 bedaquiline
rifampicin
clpC1 4040517 p.Val63Ala missense_variant 0.23 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.19 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.75 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.19 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.16 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 0.81 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.28 ethambutol Not assoc w R
embA 4245166 p.Pro645Gln missense_variant 0.27 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.23 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.24 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.22 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.24 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.27 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.24 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.21 streptomycin Not assoc w R