TB-Profiler result

Run: ERR2515164
Summary

Run ID: ERR2515164

Sample name:

Date: 2024-10-05T07:08:21.737184

Number of reads: 611557

Percentage reads mapped: 99.69

Median coverage: 32.0

Strain: lineage4.1.2;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 0.5
lineage4.1.2 Euro-American None 0.55
lineage4.4.1 Euro-American (S-type) None 0.35
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.49
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9138 p.Gln613Glu missense_variant 0.44 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
Rv0565c 657269 p.Ser68Pro missense_variant 0.48 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.61 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777416 c.1065G>T synonymous_variant 0.6 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
embR 1417140 p.Ala70Ser missense_variant 0.55 ethambutol Not assoc w R
embR 1418018 c.-671C>T upstream_gene_variant 0.56 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673249 c.-953C>T upstream_gene_variant 0.45 isoniazid
ethionamide
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
ndh 2102990 p.Val18Ala missense_variant 0.53 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2168479 p.Thr712Pro missense_variant 0.41 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.36 pyrazinamide 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
folC 2747022 p.Val193Ile missense_variant 0.58 para-aminosalicylic_acid
Rv2680 2996369 p.Asp89Asn missense_variant 0.61 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.62 ethionamide Not assoc w R - Interim
Rv3083 3448894 p.Tyr131Asp missense_variant 0.3 ethionamide Uncertain significance
Rv3083 3449642 p.Asn380Ser missense_variant 0.52 ethionamide Uncertain significance
whiB7 3568779 c.-100T>C upstream_gene_variant 0.61 kanamycin Not assoc w R
amikacin Not assoc w R
streptomycin Not assoc w R
whiB7 3568921 c.-242G>C upstream_gene_variant 0.56 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.38 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641164 p.Ile208Val missense_variant 0.65 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 0.59 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 0.72 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