TB-Profiler result

Run: ERR4798952
Summary

Run ID: ERR4798952

Sample name:

Date: 2024-03-25T20:45:32.569567

Number of reads: 4121144

Percentage reads mapped: 99.47

Median coverage: 116.0

Strain: lineage1.1.2;lineage4.1.2.1

Spoligotype:

Drug-resistance: MDR-TB

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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 0.47
lineage4.1 Euro-American None 0.52
lineage4.1.2 Euro-American None 0.51
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.51
lineage1.1 Indo-Oceanic RD239 0.47
lineage4 Euro-American None 0.52
lineage1 Indo-Oceanic RD239 0.46
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Pro Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gly406Ser Assoc w R
pyrazinamide
streptomycin gid c.102delG Assoc w R
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 761095 p.Leu430Pro missense_variant 0.44 rifampicin Assoc w R
katG 2155167 p.Ser315Thr missense_variant 0.55 isoniazid Assoc w R High-level resistance
embB 4247729 p.Gly406Ser missense_variant 0.61 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.41 streptomycin 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 6112 p.Met291Ile missense_variant 0.47 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.52 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 0.57 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.47 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 0.4 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.48 isoniazid Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.66 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.46 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575679 p.Asn111Ser missense_variant 0.59 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.53 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.4 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.41 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.43 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.64 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.43 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.62 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.38 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.38 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.57 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.4 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 0.54 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776395 p.Phe696Leu missense_variant 0.47 clofazimine Not assoc w R
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.49 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.56 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 0.45 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.55 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.48 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833875 p.Ala112Thr missense_variant 0.54 pyrazinamide
tsnR 1853974 c.369C>T synonymous_variant 0.41 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.38 linezolid Not assoc w R
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 0.37 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 0.52 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.53 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.52 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.33 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 0.47 isoniazid
kasA 2518132 c.18C>T synonymous_variant 0.52 isoniazid
eis 2714872 p.Pro154Leu missense_variant 0.45 amikacin
kanamycin
ahpC 2726051 c.-142G>A upstream_gene_variant 0.44 isoniazid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.12 capreomycin Uncertain significance
Rv2681 2996912 c.174C>T synonymous_variant 0.49 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.46 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 0.43 ethionamide Uncertain significance
whiB7 3568759 c.-80A>C upstream_gene_variant 0.5 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.41 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 0.54 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrA 3627756 c.-407A>T upstream_gene_variant 0.69 bedaquiline
rifampicin
clpC1 4040517 p.Val63Ala missense_variant 0.41 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.31 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.35 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 0.49 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.48 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.44 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 0.59 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.4 ethambutol Not assoc w R
embA 4245218 c.1986C>T synonymous_variant 0.52 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.46 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.39 ethambutol Not assoc w R
ubiA 4269031 p.Gly268Asp missense_variant 0.5 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.52 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.5 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 0.54 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 0.53 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.54 streptomycin Not assoc w R