TB-Profiler result

Run: ERR11798661
Summary

Run ID: ERR11798661

Sample name:

Date: 09-01-2024 07:28:09

Number of reads: 3525170

Percentage reads mapped: 99.52

Strain: lineage4.2.1.1

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.Thr400Ala (0.74), rpoB p.Ser450Leu (0.75)
Isoniazid R fabG1 c.-15C>T (0.72), katG p.Ser315Thr (0.78)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys88Arg (0.75), gid c.489delA (0.35)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (0.78)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.72)
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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 0.3
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 761004 p.Thr400Ala missense_variant 0.74 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.75 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.75 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.72 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.78 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 0.78 kanamycin
gid 4407713 c.489delA frameshift_variant 0.35 streptomycin
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
fgd1 491247 c.465C>T synonymous_variant 0.64
ccsA 619969 p.Val27Ile missense_variant 0.74
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 0.26
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
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877485 c.1023C>T synonymous_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249594 c.3081G>A synonymous_variant 0.76
ethA 4326632 p.His281Pro missense_variant 0.77
ethA 4328376 c.-903G>C upstream_gene_variant 0.73
whiB6 4338594 c.-73T>G upstream_gene_variant 0.7
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 0.3