TB-Profiler result

Run: ERR4819667
Summary

Run ID: ERR4819667

Sample name:

Date: 2024-04-15T11:42:30.375757

Number of reads: 5438695

Percentage reads mapped: 99.48

Median coverage: 125.0

Strain: lineage4.1.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: RR-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 0.55
lineage4.1 Euro-American None 0.42
lineage4.1.2 Euro-American None 0.46
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.45
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.56
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Tyr Assoc w R
isoniazid
ethambutol
pyrazinamide
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 761139 p.His445Tyr missense_variant 0.47 rifampicin 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
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 0.56 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
fgd1 491591 p.Lys270Met missense_variant 0.51 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.4 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 576160 c.813C>T synonymous_variant 0.51 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.31 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.46 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.51 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.42 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 781276 c.-284A>C upstream_gene_variant 0.44 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800990 p.Lys61Thr missense_variant 0.56 linezolid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473291 n.1446G>A non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance
kanamycin
capreomycin
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
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 2518919 p.Gly269Ser missense_variant 0.63 isoniazid
Rv2752c 3064535 p.Pro553Ser missense_variant 0.51 ethambutol Uncertain significance
moxifloxacin
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.54 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625005 p.Val537Ile missense_variant 0.45 bedaquiline
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877586 p.Leu308Phe missense_variant 0.59 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.49 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.56 ethambutol Not assoc w R
embC 4242182 p.Ala774Ser missense_variant 0.49 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 0.35 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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.55 streptomycin Not assoc w R