TB-Profiler result

Run: SRR6824373
Summary

Run ID: SRR6824373

Sample name:

Date: 20-10-2023 19:36:31

Number of reads: 7390084

Percentage reads mapped: 99.14

Strain: lineage4.5

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.Ser450Leu (1.00)
Isoniazid R katG c.306delT (1.00), ahpC c.-57C>T (0.99)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide
Streptomycin R rpsL p.Lys88Arg (0.13), rrs n.517C>T (0.37), rrs n.906A>G (0.42)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.1415_1427delAGATCGACGACGA (1.00)
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
lineage4.5 Euro-American H;T RD122 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.13 streptomycin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.37 streptomycin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.42 streptomycin
katG 2155805 c.306delT frameshift_variant 1.0 isoniazid
ahpC 2726136 c.-57C>T upstream_gene_variant 0.99 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326046 c.1415_1427delAGATCGACGACGA frameshift_variant 1.0 ethionamide
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 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoB 762310 p.His835Arg missense_variant 0.46
rpoC 764821 p.Trp484Cys missense_variant 0.34
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
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embC 4242098 p.Gly746Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0