TB-Profiler result

Run: ERR1035359
Summary

Run ID: ERR1035359

Sample name:

Date: 20-10-2023 21:42:07

Number of reads: 7245951

Percentage reads mapped: 98.87

Strain: lineage4.3.4.1

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.Gln497Arg (1.00)
Pyrazinamide R pncA p.Ala171Val (0.99)
Streptomycin
Fluoroquinolones R gyrA p.Ser91Pro (1.00)
Moxifloxacin R gyrA p.Ser91Pro (1.00)
Ofloxacin R gyrA p.Ser91Pro (1.00)
Levofloxacin R gyrA p.Ser91Pro (1.00)
Ciprofloxacin R gyrA p.Ser91Pro (1.00)
Aminoglycosides R rrs n.1401A>G (0.67)
Amikacin R rrs n.1401A>G (0.67)
Capreomycin R rrs n.1401A>G (0.67)
Kanamycin R rrs n.1401A>G (0.67)
Cycloserine R ald c.968_969dupAG (0.12)
Ethionamide R ethA p.Pro378Leu (0.67), ethA p.Trp289* (0.26)
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
lineage4.3.4 Euro-American (LAM) LAM RD174 0.99
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.67 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288730 p.Ala171Val missense_variant 0.99 pyrazinamide
ald 3087785 c.968_969dupAG frameshift_variant 0.12 cycloserine
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4326341 p.Pro378Leu missense_variant 0.67 ethionamide
ethA 4326608 p.Trp289* stop_gained 0.26 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 9304 p.Gly668Asp missense_variant 1.0
mshA 575744 p.Ala133Pro missense_variant 0.28
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765462 p.Asn698Ser missense_variant 0.98
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
rpoA 3878600 c.-93G>A upstream_gene_variant 0.96
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039991 c.714G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407976 p.Gly76Asp missense_variant 0.27
gid 4408138 p.Tyr22Cys missense_variant 0.57
gid 4408156 p.Leu16Arg missense_variant 1.0