TB-Profiler result

Run: ERR6358762
Summary

Run ID: ERR6358762

Sample name:

Date: 2024-04-15T21:43:14.984632

Number of reads: 7809185

Percentage reads mapped: 99.73

Median coverage: 233.0

Strain: lineage4.6.1.2;lineage4.8.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.54
lineage4.6.1.2 Euro-American RD724 0.54
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.49
lineage4.8.1 Euro-American (mainly T) RD219 0.49
lineage4.6.1 Euro-American (Uganda) RD724 0.5
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.His1002Arg Uncertain significance Mutation from literature
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA p.Gln10Arg Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1215_1224delGTTGAATTAC Assoc w R
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 0.6 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.58 isoniazid Assoc w R High-level resistance
pncA 2289213 p.Gln10Arg missense_variant 0.53 pyrazinamide Assoc w R
embB 4249518 p.His1002Arg missense_variant 0.51 ethambutol Uncertain significance Mutation from literature
embB 4249583 p.Asp1024Asn missense_variant 0.5 ethambutol Uncertain significance Mutation from literature
ethA 4326249 c.1215_1224delGTTGAATTAC frameshift_variant 0.5 ethionamide 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
dnaA 1049 p.Arg350Gln missense_variant 0.55 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7539 p.Thr80Ala missense_variant 0.54 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 0.59 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.53 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 763444 c.75T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoC 764810 p.Pro481Thr missense_variant 0.54 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
embR 1416410 p.Leu313Arg missense_variant 0.59 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.52 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.54 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.52 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.44 pyrazinamide Not assoc w R
PPE35 2170692 c.-80T>G upstream_gene_variant 0.52 pyrazinamide Uncertain significance
PPE35 2170892 c.-280G>A upstream_gene_variant 0.52 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2714308 p.Pro342Leu missense_variant 0.52 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.47 capreomycin
Rv2681 2996876 c.138A>C synonymous_variant 0.54 capreomycin Not assoc w R
Rv2752c 3065920 p.Pro91Leu missense_variant 0.56 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
fbiD 3339040 c.-78T>C upstream_gene_variant 0.47 clofazimine
pretomanid
delamanid
whiB7 3569029 c.-350A>G upstream_gene_variant 0.56 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Not assoc w R
fbiB 3642874 p.Leu447Arg missense_variant 0.52 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rpoA 3877967 p.Thr181Ala missense_variant 0.49 rifampicin Uncertain significance
glpK 4139670 p.Cys29Tyr missense_variant 0.58 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Not assoc w R
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245055 p.Thr608Asn missense_variant 0.53 ethambutol Uncertain significance
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 4338732 c.-211C>T upstream_gene_variant 0.52 capreomycin
amikacin
kanamycin
gid 4408094 p.Gly37Arg missense_variant 0.44 streptomycin Uncertain significance