TB-Profiler result

Run: ERR751448
Summary

Run ID: ERR751448

Sample name:

Date: 19-10-2023 12:52:00

Number of reads: 4777458

Percentage reads mapped: 99.61

Strain: lineage4.3.3

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.Asp435Val (0.79), rpoB p.Ser450Leu (0.22)
Isoniazid R fabG1 c.-15C>T (0.18), inhA p.Ile21Thr (0.21), katG p.Ser315Thr (0.78)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.His51Arg (0.24), pncA p.Lys48Thr (0.76)
Streptomycin
Fluoroquinolones R gyrA p.Asp94Gly (0.71)
Moxifloxacin R gyrA p.Asp94Gly (0.71)
Ofloxacin R gyrA p.Asp94Gly (0.71)
Levofloxacin R gyrA p.Asp94Gly (0.71)
Ciprofloxacin R gyrA p.Asp94Gly (0.71)
Aminoglycosides R rrs n.1401A>G (0.70)
Amikacin R rrs n.1401A>G (0.70)
Capreomycin R rrs n.1401A>G (0.70)
Kanamycin R rrs n.1401A>G (0.70)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.18), inhA p.Ile21Thr (0.21), ethA p.Pro378Leu (0.85)
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
gyrA 7582 p.Asp94Gly missense_variant 0.71 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.79 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.22 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.7 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.18 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_variant 0.21 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.78 isoniazid
pncA 2289090 p.His51Arg missense_variant 0.24 pyrazinamide
pncA 2289099 p.Lys48Thr missense_variant 0.76 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326341 p.Pro378Leu missense_variant 0.85 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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
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
rpsA 1833702 p.Asp54Ala missense_variant 0.2
rpsA 1834683 p.Ala381Val missense_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087715 c.897dupG frameshift_variant 0.77
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243392 p.Asn54Asp missense_variant 0.78
ubiA 4269731 p.Ala35Ser missense_variant 0.7
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407768 p.Leu145Phe missense_variant 0.22
gid 4407986 p.Gly73Arg missense_variant 0.73
gid 4408156 p.Leu16Arg missense_variant 1.0