TB-Profiler result

Run: ERR108464
Summary

Run ID: ERR108464

Sample name:

Date: 21-10-2023 05:59:08

Number of reads: 4624684

Percentage reads mapped: 99.44

Strain: lineage4.8;lineage4.2.1

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (0.89)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.86)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
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
lineage4.2 Euro-American H;T;LAM None 0.83
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.19
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.84
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
rpsL 781687 p.Lys43Arg missense_variant 0.86 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.89 isoniazid
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 7585 p.Ser95Thr missense_variant 0.89
gyrA 9304 p.Gly668Asp missense_variant 0.9
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 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.19
PPE35 2169879 p.Phe245Cys missense_variant 0.89
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.9
ald 3086788 c.-32T>C upstream_gene_variant 0.89
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.86
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249354 c.2841G>C synonymous_variant 0.21
embB 4249594 c.3081G>A synonymous_variant 0.79
ethR 4327937 p.Thr130Ile missense_variant 0.16
ethA 4328376 c.-903G>C upstream_gene_variant 0.87
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338598 c.-77G>C upstream_gene_variant 0.11