TB-Profiler result

Run: ERR2516568

Summary

Run ID: ERR2516568

Sample name:

Date: 19-10-2023 23:48:21

Number of reads: 2353057

Percentage reads mapped: 99.57

Strain: lineage4.1.2.1

Drug-resistance: HR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R fabG1 c.-8T>G (1.00)
Ethambutol
Pyrazinamide
Streptomycin R rrs n.905C>A (1.00)
Fluoroquinolones R gyrA p.Ser91Pro (1.00)
Moxifloxacin R gyrA p.Ser91Pro (1.00)
Ofloxacin R gyrA p.Ser91Pro (1.00)
Levofloxacin R gyrA p.Ser91Pro (1.00)
Ciprofloxacin R gyrA p.Ser91Pro (1.00)
Aminoglycosides
Amikacin R eis c.-14C>T (1.00)
Capreomycin
Kanamycin R eis c.-14C>T (1.00)
Cycloserine
Ethionamide R ethA c.766_767delTG (0.25)
Clofazimine
Para-aminosalicylic_acid R folC p.Arg49Trp (0.52), folC p.Ile43Ser (0.27)
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rrs 1472750 n.905C>A non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673432 c.-8T>G upstream_gene_variant 1.0 isoniazid
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
folC 2747454 p.Arg49Trp missense_variant 0.52 para-aminosalicylic_acid
folC 2747471 p.Ile43Ser missense_variant 0.27 para-aminosalicylic_acid
ethA 4326706 c.766_767delTG frameshift_variant 0.25 ethionamide
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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.97
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu 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
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222757 c.408G>A synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841341 p.Pro27Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ethA 4327059 p.Gly139Ser missense_variant 0.17
ethA 4327471 c.3G>A start_lost 0.52
whiB6 4338362 p.Arg54Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0