TB-Profiler result

Run: ERR2513742
Summary

Run ID: ERR2513742

Sample name:

Date: 20-10-2023 12:53:27

Number of reads: 1482079

Percentage reads mapped: 99.11

Strain: lineage4.8

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 c.36_37insGCCAGCGAGCCACCCTCGCAGAAGTCG (1.00)
Streptomycin R gid c.102delG (1.00)
Fluoroquinolones R gyrA p.Asp94Ala (0.97)
Moxifloxacin R gyrA p.Asp94Ala (0.97)
Ofloxacin R gyrA p.Asp94Ala (0.97)
Levofloxacin R gyrA p.Asp94Ala (0.97)
Ciprofloxacin R gyrA p.Asp94Ala (0.97)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.1292delT (1.00), ethA c.1292delT (1.00)
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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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.Asp94Ala missense_variant 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289205 c.36_37insGCCAGCGAGCCACCCTCGCAGAAGTCG conservative_inframe_insertion 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326181 c.1292delT frameshift_variant 1.0 ethionamide, ethionamide
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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 9647 c.2346C>T synonymous_variant 1.0
rpoB 761568 p.Ile588Val 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
rrs 1472089 n.244C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.16
PPE35 2167868 c.2745A>C synonymous_variant 0.14
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3074127 c.345G>A synonymous_variant 1.0
ald 3086987 p.Gln56His missense_variant 1.0
ald 3087894 c.1076dupT frameshift_variant 1.0
fprA 3474119 p.Met38Thr missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0