TB-Profiler result

Run: ERR3273089
Summary

Run ID: ERR3273089

Sample name:

Date: 2024-10-05T05:50:51.693960

Number of reads: 2985642

Percentage reads mapped: 99.36

Median coverage: 89.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 1.0
lineage4 Euro-American None 1.0
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.Thr380Ile Uncertain significance Mutation from literature
ahpC c.-48G>A Uncertain significance Mutation from literature
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Val125Phe Assoc w R - Interim
p.Tyr103Cys Assoc w R
p.His43Pro 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2154973 p.Thr380Ile missense_variant 1.0 isoniazid Uncertain significance Mutation from literature
pncA 2288869 p.Val125Phe missense_variant 0.22 pyrazinamide Assoc w R - Interim
pncA 2288934 p.Tyr103Cys missense_variant 0.17 pyrazinamide Assoc w R
pncA 2289114 p.His43Pro missense_variant 0.45 pyrazinamide Assoc w R - Interim
ahpC 2726145 c.-48G>A upstream_gene_variant 0.64 isoniazid Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol 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 484 p.Thr162Ala missense_variant 1.0 isoniazid
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7892 c.591G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 1.0 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
rpoC 766485 p.Val1039Ala missense_variant 0.21 rifampicin Uncertain significance
rpoC 766789 c.3420G>A synonymous_variant 0.98 rifampicin Not assoc w R - Interim
rpoC 766825 p.Lys1152Asn missense_variant 0.99 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 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 1254182 p.His118Pro missense_variant 0.7 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472176 n.331G>A non_coding_transcript_exon_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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 2154047 p.Trp689Gly missense_variant 1.0 isoniazid Uncertain significance
katG 2156199 c.-88G>A upstream_gene_variant 0.99 isoniazid
katG 2156258 c.-148_-147insA upstream_gene_variant 0.99 isoniazid
PPE35 2170568 p.Ile15Met missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pepQ 2859673 p.Ile249Ser missense_variant 1.0 bedaquiline
clofazimine
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878333 p.Val59Leu missense_variant 1.0 rifampicin
rpoA 3878575 c.-68C>T upstream_gene_variant 0.98 rifampicin Not assoc w R
rpoA 3879070 c.-563G>A upstream_gene_variant 1.0 rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 0.99 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269284 p.Ser184Ala missense_variant 0.16 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407766 p.Thr146Lys missense_variant 0.17 streptomycin Uncertain significance