TB-Profiler result

Run: SRR24256062

Summary

Run ID: SRR24256062

Sample name:

Date: 01-02-2024 15:23:50

Number of reads: 3590387

Percentage reads mapped: 99.73

Strain: lineage4.3.3

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 fabG1 c.-15C>T (0.40), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.49)
Pyrazinamide R pncA p.Thr142Met (0.41)
Streptomycin R rpsL p.Lys43Arg (0.52), rrs n.514A>C (0.40)
Fluoroquinolones R gyrA p.Asp94Gly (0.41)
Moxifloxacin R gyrA p.Asp94Gly (0.41)
Ofloxacin R gyrA p.Asp94Gly (0.41)
Levofloxacin R gyrA p.Asp94Gly (0.41)
Ciprofloxacin R gyrA p.Asp94Gly (0.41)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.40)
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 0.95
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.95
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 7582 p.Asp94Gly missense_variant 0.41 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.52 streptomycin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.4 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.4 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288817 p.Thr142Met missense_variant 0.41 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.49 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 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.97
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761998 p.Leu731Pro missense_variant 0.51
rpoC 764667 p.Gly433Ala missense_variant 0.46
rpoC 764995 c.1626C>G synonymous_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.97
fbiC 1304962 p.Trp678Gly missense_variant 0.51
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.92
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.95
folC 2746340 p.Ala420Val missense_variant 0.99
ribD 2986827 c.-12G>A upstream_gene_variant 0.43
ribD 2987502 p.Gly222Ser missense_variant 0.27
thyA 3073868 p.Thr202Ala missense_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568759 c.-80A>C upstream_gene_variant 0.44
clpC1 4038287 c.2418C>T synonymous_variant 0.92
clpC1 4038968 c.1737G>A synonymous_variant 0.94
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247717 p.Leu402Val missense_variant 0.46
ethA 4326593 p.Cys294Tyr missense_variant 0.47
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.95