TB-Profiler result

Run: ERR1034609

Summary

Run ID: ERR1034609

Sample name:

Date: 20-10-2023 22:03:00

Number of reads: 23408071

Percentage reads mapped: 99.57

Strain: lineage4.9

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.Met306Val (1.00)
Pyrazinamide R pncA p.Pro54Leu (1.00)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrA p.Asp94Asn (1.00)
Moxifloxacin R gyrA p.Asp94Asn (1.00)
Ofloxacin R gyrA p.Asp94Asn (1.00)
Levofloxacin R gyrA p.Asp94Asn (1.00)
Ciprofloxacin R gyrA p.Asp94Asn (1.00)
Aminoglycosides
Amikacin R eis c.-14C>T (0.97)
Capreomycin
Kanamycin R eis c.-14C>T (0.97)
Cycloserine
Ethionamide R ethA c.404_405insAT (0.96)
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
lineage4.9 Euro-American (H37Rv-like) T1 None 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 7581 p.Asp94Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289081 p.Pro54Leu missense_variant 1.0 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 0.97 kanamycin, amikacin
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327069 c.404_405insAT frameshift_variant 0.96 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
mshA 576400 c.1053C>T synonymous_variant 1.0
rpoB 761461 p.Arg552Leu missense_variant 1.0
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 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3087367 p.Ala183Val missense_variant 1.0
rpoA 3877536 c.972C>T synonymous_variant 1.0
ubiA 4269124 p.Ala237Val missense_variant 1.0
whiB6 4338307 p.Ala72Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0