TB-Profiler result

Run: ERR11465134
Summary

Run ID: ERR11465134

Sample name:

Date: 2024-04-15T03:51:30.137471

Number of reads: 8425733

Percentage reads mapped: 99.65

Median coverage: 201.0

Strain: lineage4.1.2.1;lineage4.4.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.37
lineage4.1.2 Euro-American None 0.38
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.39
lineage4.4.1 Euro-American (S-type) None 0.64
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.63
lineage4.4 Euro-American None 0.63
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
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
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 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9138 p.Gln613Glu missense_variant 0.63 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
fgd1 491591 p.Lys270Met missense_variant 0.39 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.39 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.15 ethionamide
isoniazid
Rv0565c 657269 p.Ser68Pro missense_variant 0.36 ethionamide Uncertain significance
hadA 732002 p.Ile25Val missense_variant 0.43 isoniazid
rpoB 760115 c.309C>T synonymous_variant 0.35 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.52 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777416 c.1065G>T synonymous_variant 0.59 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 0.44 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
embR 1416821 p.Ala176Gly missense_variant 0.4 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.98 capreomycin Not assoc w R
ndh 2102990 p.Val18Ala missense_variant 0.61 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
PPE35 2168479 p.Thr712Pro missense_variant 0.49 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.8 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289270 c.-29G>A upstream_gene_variant 0.61 pyrazinamide
kasA 2518076 c.-39C>T upstream_gene_variant 0.3 isoniazid
Rv2477c 2784617 c.-575T>C upstream_gene_variant 0.43 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.6 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 0.58 streptomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.69 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.56 ethambutol Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.43 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.38 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.25 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.15 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.19 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.19 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.16 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.2 ethambutol Not assoc w R - Interim
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