TB-Profiler result

Run: ERR4813796
Summary

Run ID: ERR4813796

Sample name:

Date: 2024-04-14T23:51:02.335912

Number of reads: 2317266

Percentage reads mapped: 99.64

Median coverage: 69.0

Strain: lineage4.1.1.3;lineage4.3.2

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 0.72
lineage4.3.2 Euro-American (LAM) None 0.73
lineage4.1 Euro-American None 0.31
lineage4.1.1.3 Euro-American (X-type) RD193 0.31
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.3
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
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 761155 p.Ser450Leu missense_variant 0.76 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
dnaA 290 p.Gly97Ala missense_variant 0.79 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 0.99 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
Rv0010c 13535 c.24T>C synonymous_variant 0.71 isoniazid Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.31 ethionamide Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.68 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.39 rifampicin Not assoc w R
rpoC 766488 p.Pro1040Arg missense_variant 0.55 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
Rv1129c 1254582 c.-48A>G upstream_gene_variant 0.69 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.68 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
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 2155683 p.Lys143Asn missense_variant 0.71 isoniazid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289017 c.225T>C synonymous_variant 0.28 pyrazinamide Not assoc w R - Interim
kasA 2519131 c.1017G>T synonymous_variant 0.75 isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.69 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.98 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
ddn 3986910 p.Arg23Trp missense_variant 0.68 delamanid Uncertain significance
pretomanid
clpC1 4038287 c.2418C>T synonymous_variant 0.81 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 0.31 ethambutol Not assoc w R
embB 4248914 p.Ala801Thr missense_variant 0.72 ethambutol Uncertain significance
embB 4249408 c.2895G>A synonymous_variant 0.24 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 0.6 streptomycin Not assoc w R