TB-Profiler result

Run: ERR1034603

Summary

Run ID: ERR1034603

Sample name:

Date: 20-10-2023 22:02:59

Number of reads: 24744955

Percentage reads mapped: 99.31

Strain: lineage4.1.1.3

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.Ser450Leu (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Asp328Tyr (1.00)
Pyrazinamide R pncA p.Ile6Met (1.00)
Streptomycin
Fluoroquinolones R gyrB p.Thr500Asn (1.00), gyrA p.Ala90Val (0.17), gyrA p.Asp94Tyr (0.68)
Moxifloxacin R gyrB p.Thr500Asn (1.00), gyrA p.Ala90Val (0.17), gyrA p.Asp94Tyr (0.68)
Ofloxacin R gyrB p.Thr500Asn (1.00), gyrA p.Ala90Val (0.17), gyrA p.Asp94Tyr (0.68)
Levofloxacin R gyrB p.Thr500Asn (1.00), gyrA p.Ala90Val (0.17), gyrA p.Asp94Tyr (0.68)
Ciprofloxacin R gyrB p.Thr500Asn (1.00), gyrA p.Ala90Val (0.17), gyrA p.Asp94Tyr (0.68)
Aminoglycosides R rrs n.1401A>G (0.95)
Amikacin R rrs n.1401A>G (0.95)
Capreomycin R rrs n.1401A>G (0.95)
Kanamycin R rrs n.1401A>G (0.95)
Cycloserine
Ethionamide R ethA c.150delT (1.00)
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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
gyrB 6738 p.Thr500Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 0.17 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Tyr missense_variant 0.68 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.95 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289224 p.Ile6Met missense_variant 1.0 pyrazinamide
embB 4247495 p.Asp328Tyr missense_variant 1.0 ethambutol
ethA 4327323 c.150delT frameshift_variant 1.0 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
rpoB 761460 p.Arg552Ser 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 1416187 c.1161C>T synonymous_variant 1.0
embR 1417195 c.153A>G synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102627 c.406_415delCCCGGCATGA frameshift_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067949 c.-4C>T upstream_gene_variant 0.61
thyX 3067959 c.-14C>G upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087388 c.572dupG frameshift_variant 0.92
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474504 c.498G>A synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243218 c.-15C>G upstream_gene_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407980 p.Pro75Ser missense_variant 1.0