TB-Profiler result

Run: ERR1035277

Summary

Run ID: ERR1035277

Sample name:

Date: 20-10-2023 21:37:25

Number of reads: 6995131

Percentage reads mapped: 99.59

Strain: lineage4.3.2

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.Ser450Leu (0.98)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Asp354Ala (0.99)
Pyrazinamide R pncA p.Gly17Asp (1.00)
Streptomycin R rrs n.514A>T (1.00)
Fluoroquinolones R gyrA p.Ala90Val (0.98)
Moxifloxacin R gyrA p.Ala90Val (0.98)
Ofloxacin R gyrA p.Ala90Val (0.98)
Levofloxacin R gyrA p.Ala90Val (0.98)
Ciprofloxacin R gyrA p.Ala90Val (0.98)
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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.2 Euro-American (LAM) LAM3 None 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 7570 p.Ala90Val missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin
rrs 1472359 n.514A>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289192 p.Gly17Asp missense_variant 1.0 pyrazinamide
embB 4247574 p.Asp354Ala missense_variant 0.99 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 7584 p.Ser95Thr missense_variant 0.77
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575960 p.Gln205Ser missense_variant 1.0
rpoB 762300 p.Lys832Gln missense_variant 0.9
rpoB 763092 p.Val1096Met missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519131 c.1017G>T synonymous_variant 1.0
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
ddn 3986910 p.Arg23Trp missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243225 c.-8C>T upstream_gene_variant 1.0
ethR 4326670 c.-879G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.99