TB-Profiler result

Run: ERR8975439
Summary

Run ID: ERR8975439

Sample name:

Date: 20-10-2023 15:59:33

Number of reads: 1812347

Percentage reads mapped: 99.72

Strain: lineage4.4.1.1;lineage4.3.4.1

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R fabG1 c.-15C>T (0.33)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-13A>G (0.25), eis c.-13A>G (0.25)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.33)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 0.28
lineage4.4 Euro-American S;T None 0.67
lineage4.4.1 Euro-American (S-type) S;T None 0.66
lineage4.3.4 Euro-American (LAM) LAM RD174 0.37
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.32
lineage4.4.1.1 Euro-American S;Orphans None 0.65
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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.33 isoniazid, ethionamide
eis 2715345 c.-13A>G upstream_gene_variant 0.25 kanamycin, kanamycin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 0.74
gyrA 9304 p.Gly668Asp missense_variant 0.98
rpoC 764995 c.1626C>G synonymous_variant 0.3
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 0.65
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.54
PPE35 2168479 p.Thr712Pro missense_variant 0.62
PPE35 2169840 p.Gly258Asp missense_variant 0.52
Rv1979c 2222854 p.Ile104Thr missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.46
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 0.68
Rv3236c 3612009 p.Ala370Thr missense_variant 0.31
Rv3236c 3612665 p.Val151Ala missense_variant 0.62
clpC1 4038287 c.2418C>T synonymous_variant 0.22
clpC1 4039991 c.714G>A synonymous_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.34