TB-Profiler result

Run: ERR144613
Summary

Run ID: ERR144613

Sample name:

Date: 20-10-2023 15:10:16

Number of reads: 13567495

Percentage reads mapped: 99.56

Strain: lineage4.3.4.1;lineage4.1

Drug-resistance: RR-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 R rpoB p.His445Asn (0.11)
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.12
lineage4.1 Euro-American T;X;H None 0.77
lineage4.3.4 Euro-American (LAM) LAM RD174 0.13
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.14
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
rpoB 761139 p.His445Asn missense_variant 0.11 rifampicin
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 0.91
gyrA 9304 p.Gly668Asp missense_variant 0.93
rpoC 763783 c.414G>A synonymous_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 0.81
rpoC 765325 c.1956C>T synonymous_variant 0.15
rpoC 765435 p.His689Arg missense_variant 0.76
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 1472954 n.1109T>C non_coding_transcript_exon_variant 0.77
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168147 c.2466A>G synonymous_variant 0.15
Rv1979c 2223123 c.42G>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746540 c.1059G>A synonymous_variant 0.14
thyX 3067487 p.Lys153Asn missense_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 0.92
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.91
Rv3236c 3612009 p.Ala370Thr missense_variant 0.12
fbiB 3642576 p.Val348Ile missense_variant 0.79
clpC1 4038287 c.2418C>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.77
embB 4249408 c.2895G>A synonymous_variant 0.76
ethR 4326910 c.-639G>A upstream_gene_variant 0.76
whiB6 4338550 c.-29A>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.14