TB-Profiler result

Run: SAMEA5569996
Summary

Run ID: SAMEA5569996

Sample name:

Date: 2024-04-15T13:30:10.701406

Number of reads: 8160398

Percentage reads mapped: 99.73

Median coverage: 248.0

Strain: lineage4.3.2;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4.3.2 Euro-American (LAM) None 0.46
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.54
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 embA c.-16C>G Uncertain significance Mutation from literature
pyrazinamide pncA p.Gly97Asp Assoc w R
streptomycin rpsL p.Lys88Thr Uncertain significance Mutation from literature
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 761155 p.Ser450Leu missense_variant 0.53 rifampicin Assoc w R
rpsL 781822 p.Lys88Thr missense_variant 0.48 streptomycin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.54 isoniazid Assoc w R High-level resistance
pncA 2288952 p.Gly97Asp missense_variant 0.54 pyrazinamide Assoc w R
embA 4243217 c.-16C>G upstream_gene_variant 0.52 ethambutol Uncertain significance Mutation from literature
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 82 p.Asp28His missense_variant 0.51 isoniazid 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.49 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
mshA 574862 c.-486T>C upstream_gene_variant 0.55 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 657730 c.-260A>C upstream_gene_variant 0.49 ethionamide
rpoB 761880 p.Ala692Thr missense_variant 0.59 rifampicin Uncertain significance
rpoC 763958 p.Val197Ile missense_variant 0.41 rifampicin Uncertain significance
rpoC 764840 p.Ile491Val missense_variant 0.59 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
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
rplC 801151 p.Thr115Ala missense_variant 0.47 linezolid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.48 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rpsA 1834836 p.Met432Thr missense_variant 0.55 pyrazinamide Not assoc w R - Interim
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
katG 2154459 c.1653C>T synonymous_variant 0.51 isoniazid 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 2518919 p.Gly269Ser missense_variant 0.55 isoniazid
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
panD 4044824 c.-543C>G upstream_gene_variant 0.55 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326207 p.Gly423Arg missense_variant 0.44 ethionamide Uncertain significance
ethA 4327350 p.Gly42Ser missense_variant 0.59 ethionamide 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 1.0 capreomycin
amikacin
kanamycin
gid 4407720 c.483C>G synonymous_variant 0.57 streptomycin Not assoc w R - Interim
gid 4408003 p.Asp67Gly missense_variant 0.56 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R