TB-Profiler result

Run: ERR1035274

Summary

Run ID: ERR1035274

Sample name:

Date: 20-10-2023 21:33:14

Number of reads: 6770388

Percentage reads mapped: 99.56

Strain: lineage4.6.4

Drug-resistance: Pre-XDR-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 p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Thr76Pro (1.00)
Streptomycin
Fluoroquinolones R gyrA p.Ala90Val (0.92)
Moxifloxacin R gyrA p.Ala90Val (0.92)
Ofloxacin R gyrA p.Ala90Val (0.92)
Levofloxacin R gyrA p.Ala90Val (0.92)
Ciprofloxacin R gyrA p.Ala90Val (0.92)
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
lineage4.6 Euro-American T;LAM None 0.99
lineage4.6.4 Euro-American T;LAM None 0.99
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
gyrA 7570 p.Ala90Val missense_variant 0.92 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val 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 762715 p.Val970Ala missense_variant 0.99
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
rrl 1474750 n.1093C>T non_coding_transcript_exon_variant 1.0
inhA 1674685 p.Thr162Ala missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222795 p.Asp124Asn missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288792 c.450C>T synonymous_variant 1.0
eis 2714393 p.Val314Leu missense_variant 0.99
fbiD 3339073 c.-45G>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326693 p.Arg261Trp missense_variant 1.0
whiB6 4338546 c.-25G>C upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407946 p.Leu86Pro missense_variant 0.99