TB-Profiler result

Run: ERR11488656
Summary

Run ID: ERR11488656

Sample name:

Date: 06-01-2024 22:51:19

Number of reads: 3080427

Percentage reads mapped: 99.76

Strain: lineage4.9.1

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.Gln432Pro (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Leu (0.42)
Pyrazinamide
Streptomycin
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
Aminoglycosides
Amikacin
Capreomycin R tlyA c.731_732dupGC (0.47)
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
lineage4.9 Euro-American (H37Rv-like) T1 None 1.0
lineage4.9.1 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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761101 p.Gln432Pro missense_variant 1.0 rifampicin
tlyA 1918667 c.731_732dupGC frameshift_variant 0.47 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Leu missense_variant 0.42 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 8095 p.Gly265Val missense_variant 1.0
gyrA 8978 c.1677C>T synonymous_variant 1.0
rpoC 764666 p.Gly433Ser missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417416 c.-69G>A 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
pncA 2289138 p.Leu35Arg missense_variant 1.0
ald 3087308 c.492dupC frameshift_variant 0.54
ald 3087648 c.830_831dupGC frameshift_variant 0.43
fbiD 3339385 p.Asp90Asn missense_variant 1.0
ethA 4327277 p.Phe66Ser missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407946 p.Leu86His missense_variant 0.99