TB-Profiler result

Run: ERR2510453
Summary

Run ID: ERR2510453

Sample name:

Date: 20-10-2023 07:20:58

Number of reads: 1521821

Percentage reads mapped: 99.77

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), embB p.Gln497Pro (1.00)
Pyrazinamide R pncA p.Val7Phe (1.00)
Streptomycin
Fluoroquinolones R gyrB p.Ser447Phe (0.22), gyrA p.Ala90Val (0.81), gyrA p.Asp94Ala (1.00)
Moxifloxacin R gyrB p.Ser447Phe (0.22), gyrA p.Ala90Val (0.81), gyrA p.Asp94Ala (1.00)
Ofloxacin R gyrB p.Ser447Phe (0.22), gyrA p.Ala90Val (0.81), gyrA p.Asp94Ala (1.00)
Levofloxacin R gyrB p.Ser447Phe (0.22), gyrA p.Ala90Val (0.81), gyrA p.Asp94Ala (1.00)
Ciprofloxacin R gyrB p.Ser447Phe (0.22), gyrA p.Ala90Val (0.81), gyrA p.Asp94Ala (1.00)
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
lineage4.8 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
gyrB 6579 p.Ser447Phe missense_variant 0.22 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 0.81 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289223 p.Val7Phe missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
embB 4248003 p.Gln497Pro missense_variant 1.0 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 0.98
rpoB 759939 p.Pro45Ser missense_variant 1.0
rpoC 764580 p.Asp404Gly missense_variant 0.97
rpoC 765331 c.1962C>T synonymous_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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407973 p.Val77Ala missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0