TB-Profiler result

Run: SRR6824434
Summary

Run ID: SRR6824434

Sample name:

Date: 20-10-2023 19:36:57

Number of reads: 10855674

Percentage reads mapped: 99.4

Strain: lineage4.4.2

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.Leu452Pro (1.00)
Isoniazid R katG c.371delG (1.00), katG c.371delG (1.00), ahpC c.-52C>T (1.00)
Ethambutol R embA c.-12C>T (1.00), embB p.Gln497Arg (0.99)
Pyrazinamide
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
lineage4.4.2 Euro-American T1;T2 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 761161 p.Leu452Pro missense_variant 1.0 rifampicin
katG 2155740 c.371delG frameshift_variant 1.0 isoniazid, isoniazid
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.99 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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779177 p.Ser63Asn missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746936 c.663T>C synonymous_variant 0.17
Rv2752c 3066051 c.88_140delAACATGACGGTTTTCGAACACCTGGGCCGACTGTTGATTATCGACTGCGGTGT frameshift_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448348 c.-156G>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038194 c.2511G>A synonymous_variant 0.99
clpC1 4039376 p.Asp443Glu missense_variant 0.99
clpC1 4039873 p.Thr278Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 0.99
embB 4247249 p.Gly246Arg missense_variant 0.99
aftB 4268928 c.-92C>T upstream_gene_variant 0.99
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
whiB6 4338422 p.Cys34Ser missense_variant 0.11
whiB6 4338460 p.Met21Thr missense_variant 0.86
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv2752c 3066051 c.87_140delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG disruptive_inframe_deletion 1.0