TB-Profiler result

Run: ERR144613
Summary

Run ID: ERR144613

Sample name:

Date: 2024-10-04T10:44:26.527076

Number of reads: 13567495

Percentage reads mapped: 99.56

Median coverage: 300.0

Strain: lineage4.1;lineage4.3.4.1

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 0.12
lineage4.1 Euro-American None 0.77
lineage4.3.4.1 Euro-American (LAM) RD174 0.14
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.13
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asn 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.His445Asn missense_variant 0.11 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 0.91 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.93 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13717 c.-159T>G upstream_gene_variant 0.78 isoniazid
Rv0565c 657269 p.Ser68Pro missense_variant 0.78 ethionamide Uncertain significance
rpoC 763783 c.414G>A synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.13 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.81 rifampicin Not assoc w R
rpoC 765325 c.1956C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765435 p.His689Arg missense_variant 0.76 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
rplC 800219 c.-590T>C upstream_gene_variant 0.77 linezolid
sigE 1364434 p.Arg8Trp missense_variant 0.14 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.77 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.9 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168147 c.2466A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
Rv1979c 2223123 c.42G>A synonymous_variant 0.14 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
folC 2746540 c.1059G>A synonymous_variant 0.14 para-aminosalicylic_acid
Rv2681 2996821 p.Gly28Ala missense_variant 0.11 capreomycin Uncertain significance
thyX 3067487 p.Lys153Asn missense_variant 0.13 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.14 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.92 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.12 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.91 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3642576 p.Val348Ile missense_variant 0.79 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.12 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.77 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.76 ethambutol Not assoc w R
ethR 4326910 c.-639G>A upstream_gene_variant 0.76 ethionamide
whiB6 4338550 c.-29A>T upstream_gene_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 0.91 kanamycin
capreomycin
amikacin
whiB6 4338735 c.-214C>G upstream_gene_variant 0.12 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.14 streptomycin Not assoc w R