TB-Profiler result

Run: ERR1034659
Summary

Run ID: ERR1034659

Sample name:

Date: 20-10-2023 21:43:42

Number of reads: 3119894

Percentage reads mapped: 99.73

Strain: lineage4.4.1.1

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Val170Phe (1.00)
Isoniazid R katG c.1338_1342dupCCACG (0.97), katG c.1328dupC (1.00), katG c.607_608dupAC (0.23), katG c.596dupG (0.23)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA c.384_385dupCG (0.74), pncA p.Tyr103Cys (0.46)
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
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
rpoB 760314 p.Val170Phe missense_variant 1.0 rifampicin
katG 2154769 c.1338_1342dupCCACG frameshift_variant 0.97 isoniazid
katG 2154783 c.1328dupC frameshift_variant 1.0 isoniazid
katG 2155503 c.607_608dupAC frameshift_variant 0.23 isoniazid
katG 2155515 c.596dupG frameshift_variant 0.23 isoniazid
pncA 2288856 c.384_385dupCG frameshift_variant 0.74 pyrazinamide
pncA 2288934 p.Tyr103Cys missense_variant 0.46 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 9304 p.Gly668Asp missense_variant 1.0
rpoB 760935 p.Glu377Lys missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
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 1.0
katG 2154047 p.Trp689Gly missense_variant 0.27
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2222880 c.284dupG frameshift_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860436 c.-18C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407804 p.Ala133Gly missense_variant 1.0
gid 4408072 p.Leu44Pro missense_variant 0.79