TB-Profiler result

Run: ERR3335771
Summary

Run ID: ERR3335771

Sample name:

Date: 21-10-2023 15:17:13

Number of reads: 6669320

Percentage reads mapped: 99.5

Strain: lineage4.5

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 (0.97)
Isoniazid R fabG1 c.-15C>T (0.98), ahpC c.-54C>T (0.97)
Ethambutol R embB p.Met306Ile (0.98), embB p.Gly406Asp (0.97)
Pyrazinamide R pncA p.Gly78Ser (0.98)
Streptomycin R rrs n.514A>C (0.96)
Fluoroquinolones R gyrA p.Asp94Asn (0.94)
Moxifloxacin R gyrA p.Asp94Asn (0.94)
Ofloxacin R gyrA p.Asp94Asn (0.94)
Levofloxacin R gyrA p.Asp94Asn (0.94)
Ciprofloxacin R gyrA p.Asp94Asn (0.94)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.98), ethA p.Gln269* (0.99)
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 0.97
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 7581 p.Asp94Asn missense_variant 0.94 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.96 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.98 isoniazid, ethionamide
pncA 2289010 p.Gly78Ser missense_variant 0.98 pyrazinamide
ahpC 2726139 c.-54C>T upstream_gene_variant 0.97 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.98 ethambutol
embB 4247730 p.Gly406Asp missense_variant 0.97 ethambutol
ethA 4326669 p.Gln269* stop_gained 0.99 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 0.98
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 0.98
rpoC 764817 p.Val483Gly missense_variant 0.97
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 0.98
embR 1416545 p.Thr268Ile missense_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155787 p.Ala109Thr missense_variant 0.97
PPE35 2169124 p.Thr497Ala missense_variant 0.98
PPE35 2170568 p.Ile15Met missense_variant 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086739 c.-80delA upstream_gene_variant 0.96
Rv3083 3449393 p.Leu297Ser missense_variant 0.96
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474376 p.Ala124Thr missense_variant 0.96
rpoA 3878575 c.-68C>T upstream_gene_variant 0.97
clpC1 4038318 p.Pro796Leu missense_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338218 p.Asn102Asp missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407604 p.Ala200Glu missense_variant 0.97