TB-Profiler result

Run: ERR4797059

Summary

Run ID: ERR4797059

Sample name:

Date: 20-10-2023 02:10:32

Number of reads: 4719211

Percentage reads mapped: 99.6

Strain: lineage4.1.2

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 (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embA c.-16C>T (1.00), embB p.Asp1024Asn (1.00)
Pyrazinamide R pncA p.Pro69Arg (1.00)
Streptomycin R gid p.Leu79Ser (1.00)
Fluoroquinolones R gyrA p.Ala90Val (1.00), gyrA p.Asp94Asn (0.87)
Moxifloxacin R gyrA p.Ala90Val (1.00), gyrA p.Asp94Asn (0.87)
Ofloxacin R gyrA p.Ala90Val (1.00), gyrA p.Asp94Asn (0.87)
Levofloxacin R gyrA p.Ala90Val (1.00), gyrA p.Asp94Asn (0.87)
Ciprofloxacin R gyrA p.Ala90Val (1.00), gyrA p.Asp94Asn (0.87)
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Asn missense_variant 0.87 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289036 p.Pro69Arg missense_variant 1.0 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin
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
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417140 p.Ala70Ser missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673249 c.-191C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155870 p.Glu81Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747022 p.Val193Ile missense_variant 1.0
Rv2752c 3065346 c.846T>G synonymous_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448894 p.Tyr131Asp missense_variant 1.0
Rv3083 3449642 p.Asn380Ser missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641164 p.Ile208Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
aftB 4268861 c.-25T>C upstream_gene_variant 1.0
ethA 4326257 p.Leu406Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0