TB-Profiler result

Run: ERR4829900
Summary

Run ID: ERR4829900

Sample name:

Date: 20-10-2023 06:35:53

Number of reads: 3387175

Percentage reads mapped: 99.68

Strain: lineage4.8;lineage4.7

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 katG p.Ser315Thr (0.18)
Ethambutol
Pyrazinamide R pncA c.-11A>G (0.18)
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
lineage4.7 Euro-American (mainly T) T1;T5 None 0.83
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.2
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
katG 2155168 p.Ser315Thr missense_variant 0.18 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.18 pyrazinamide
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 7762 p.Pro154Leu missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781443 c.-117T>G upstream_gene_variant 0.88
embR 1416757 c.591G>A synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.8
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155971 c.141A>G synonymous_variant 0.18
PPE35 2168149 p.Pro822Ser missense_variant 0.15
PPE35 2170675 c.-63G>C upstream_gene_variant 0.9
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859961 p.Ala153Gly missense_variant 0.74
Rv3083 3448322 c.-182G>A upstream_gene_variant 0.22
rpoA 3877547 p.Ala321Ser missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249732 c.3219C>G synonymous_variant 0.95
whiB6 4338595 c.-75delG upstream_gene_variant 1.0