TB-Profiler result

Run: ERR2706941
Summary

Run ID: ERR2706941

Sample name:

Date: 2024-04-16T07:03:14.674063

Number of reads: 3745408

Percentage reads mapped: 99.59

Median coverage: 116.0

Strain: lineage4

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 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.His445Thr Assoc w R - Interim
isoniazid
ethambutol embB p.Asp328Tyr Assoc w R
pyrazinamide pncA p.Ala146Thr Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.253dupG Assoc w R
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.His445Thr missense_variant 0.99 rifampicin Assoc w R - Interim
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
pncA 2288806 p.Ala146Thr missense_variant 1.0 pyrazinamide Assoc w R
embB 4247495 p.Asp328Tyr missense_variant 1.0 ethambutol Assoc w R
ethA 4327220 c.253dupG frameshift_variant 1.0 ethionamide 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 1057 p.Val353Leu missense_variant 1.0 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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
rplC 800977 p.Ile57Val missense_variant 1.0 linezolid
Rv1129c 1253754 p.Thr261Pro missense_variant 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
fbiC 1305457 p.Pro843Ala missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154980 c.1132C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
katG 2155178 p.Ala312Pro missense_variant 1.0 isoniazid Uncertain significance
PPE35 2170811 c.-199C>T upstream_gene_variant 1.0 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518265 p.Val51Ile missense_variant 0.99 isoniazid
eis 2715223 p.Arg37Gln missense_variant 1.0 amikacin
kanamycin Uncertain significance
Rv3083 3449145 c.642G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4268076 p.Met254Ala missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269121 p.Phe238Ser missense_variant 0.97 ethambutol Uncertain significance
ubiA 4269188 p.Thr216Ala missense_variant 0.95 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R