TB-Profiler result

Run: ERR9806872
Summary

Run ID: ERR9806872

Sample name:

Date: 18-05-2023 17:28:24

Number of reads: 1683714

Percentage reads mapped: 99.71

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 inhA c.-154G>A (0.95), inhA p.Ser94Ala (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Pro404Ser (1.00)
Pyrazinamide R pncA c.468_499delGGTGGACCTGACAGCGGGTGTGTCGGCCGATA (1.00)
Streptomycin
Fluoroquinolones R gyrB p.Ile486Leu (1.00)
Moxifloxacin R gyrB p.Ile486Leu (1.00)
Ofloxacin R gyrB p.Ile486Leu (1.00)
Levofloxacin R gyrB p.Ile486Leu (1.00)
Ciprofloxacin R gyrB p.Ile486Leu (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R inhA c.-154G>A (0.95), inhA p.Ser94Ala (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
gyrB 6695 p.Ile486Leu missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 0.95 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288742 c.468_499delGGTGGACCTGACAGCGGGTGTGTCGGCCGATA frameshift_variant 1.0 pyrazinamide
embB 4247723 p.Pro404Ser 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
gyrB 6743 p.Val502Phe missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779677 c.-772G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305471 c.2541C>T synonymous_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 2168867 c.1746G>A synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
alr 3840764 c.657G>C synonymous_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0