TB-Profiler result

Run: ERR8699184
Summary

Run ID: ERR8699184

Sample name:

Date: 2024-10-03T20:20:12.929016

Number of reads: 3308669

Percentage reads mapped: 99.68

Median coverage: 100.0

Strain: lineage4.1.1.3;lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Other

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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 0.51
lineage4.1 Euro-American None 0.52
lineage4.1.1.3 Euro-American (X-type) RD193 0.49
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.49
lineage4.1.1 Euro-American (X-type) None 0.49
lineage4.3.4 Euro-American (LAM) RD174 0.51
lineage4.3.4.2 Euro-American (LAM) RD174 0.5
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide pncA p.Cys14Arg Assoc w R
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
pncA 2289202 p.Cys14Arg missense_variant 0.57 pyrazinamide 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
gyrB 6140 p.Val301Leu missense_variant 0.5 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.49 ethionamide Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.56 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.51 rifampicin Not assoc w R
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
rpsL 781435 c.-125G>C upstream_gene_variant 0.58 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.54 linezolid
rrs 1471659 n.-187C>T upstream_gene_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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2477c 2783677 p.Met122Ile missense_variant 0.44 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2752c 3066481 c.-290C>T upstream_gene_variant 0.53 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyX 3067293 p.Gln218Arg missense_variant 0.55 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.41 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.54 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.51 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.5 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 0.54 ethambutol Not assoc w R
embB 4248838 c.2326_2331dupCCCTTG conservative_inframe_insertion 0.46 ethambutol Uncertain significance
embB 4249408 c.2895G>A synonymous_variant 0.49 ethambutol Not assoc w R
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 4407798 c.405G>T synonymous_variant 0.46 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.48 streptomycin Not assoc w R