TB-Profiler result

Run: ERR2510592

Summary

Run ID: ERR2510592

Sample name:

Date: 20-10-2023 07:23:47

Number of reads: 1184009

Percentage reads mapped: 99.61

Strain: lineage4.6.2.2

Drug-resistance: Pre-XDR-TB


Download CSV Download TXT Download PDF Download JSON
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
Pyrazinamide
Streptomycin R rrs n.514A>C (1.00)
Fluoroquinolones R gyrA p.Asp94Gly (0.45)
Moxifloxacin R gyrA p.Asp94Gly (0.45)
Ofloxacin R gyrA p.Asp94Gly (0.45)
Levofloxacin R gyrA p.Asp94Gly (0.45)
Ciprofloxacin R gyrA p.Asp94Gly (0.45)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (1.00)
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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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 0.45 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu 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
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
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 6358 c.-944C>T upstream_gene_variant 1.0
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 762715 p.Val970Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_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 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289102 p.Thr47Ile missense_variant 1.0
thyX 3067474 p.Pro158Ala missense_variant 1.0
thyA 3073859 p.Asp205Tyr missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
Rv3083 3449073 c.570C>G synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245227 c.1995C>T synonymous_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 1.0
ubiA 4269319 p.Leu172Gln missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338473 c.49A>C synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0