TB-Profiler result

Run: ERR027465
Summary

Run ID: ERR027465

Sample name:

Date: 2024-10-04T12:36:46.137869

Number of reads: 3005871

Percentage reads mapped: 99.79

Median coverage: 38.0

Strain: lineage2.2.1;lineage4.9

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.29
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.43
lineage2.2 East-Asian (Beijing) RD105;RD207 0.36
lineage4 Euro-American None 0.65
lineage4.9 Euro-American (H37Rv-like) None 0.58
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoC p.Leu527Val Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1010delT 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
rpoC 764948 p.Leu527Val missense_variant 0.41 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.57 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.41 isoniazid Assoc w R High-level resistance
ethA 4326463 c.1010delT frameshift_variant 0.32 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
gyrA 7362 p.Glu21Gln missense_variant 0.33 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.45 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.42 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.41 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.37 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.42 ethionamide Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 0.48 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.34 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.35 bedaquiline
clofazimine
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.46 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.5 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.31 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.55 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.4 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.41 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086731 c.-89A>G upstream_gene_variant 0.39 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.56 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.48 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640243 c.-300T>C upstream_gene_variant 0.27 pretomanid
delamanid
clofazimine
embA 4243346 c.114A>G synonymous_variant 0.25 ethambutol Not assoc w R - Interim
whiB6 4338371 p.Thr51Pro missense_variant 0.37 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.37 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.32 streptomycin Not assoc w R