TB-Profiler result

Run: ERR4800303

Summary

Run ID: ERR4800303

Sample name:

Date: 20-10-2023 04:16:39

Number of reads: 1578470

Percentage reads mapped: 99.43

Strain: lineage4.1.2.1

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.Leu430Arg (1.00), rpoB p.Asp435Tyr (1.00)
Isoniazid R katG p.Ser315Thr (1.00), ahpC c.-54C>T (1.00)
Ethambutol R embB p.Gln497Arg (0.98)
Pyrazinamide R pncA p.Tyr34* (0.96)
Streptomycin R rrs n.514A>C (1.00)
Fluoroquinolones R gyrA p.Asp94Tyr (1.00)
Moxifloxacin R gyrA p.Asp94Tyr (1.00)
Ofloxacin R gyrA p.Asp94Tyr (1.00)
Levofloxacin R gyrA p.Asp94Tyr (1.00)
Ciprofloxacin R gyrA p.Asp94Tyr (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
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 0.98
lineage4.1.2 Euro-American T;H None 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.98
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.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Arg missense_variant 1.0 rifampicin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289140 p.Tyr34* stop_gained 0.96 pyrazinamide
ahpC 2726139 c.-54C>T upstream_gene_variant 1.0 isoniazid
embB 4248003 p.Gln497Arg missense_variant 0.98 ethambutol
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
fgd1 491591 p.Lys270Met missense_variant 0.98
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 0.98
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
Rv1258c 1407079 c.261delC frameshift_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.87
thyA 3074495 c.-24C>T upstream_gene_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474303 c.297C>T synonymous_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.94
ethA 4326356 p.Met373Thr missense_variant 0.98
ethR 4327918 p.Gly124Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0