TB-Profiler result

Run: ERR8975000
Summary

Run ID: ERR8975000

Sample name:

Date: 20-10-2023 15:38:20

Number of reads: 2415440

Percentage reads mapped: 99.75

Strain: lineage4.4.1.1.1

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.Ile491Phe (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Gln497Arg (1.00)
Pyrazinamide R pncA c.-11A>G (1.00)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrB p.Glu501Asp (0.86), gyrA p.Ala90Val (0.13)
Moxifloxacin R gyrB p.Glu501Asp (0.86), gyrA p.Ala90Val (0.13)
Ofloxacin R gyrB p.Glu501Asp (0.86), gyrA p.Ala90Val (0.13)
Levofloxacin R gyrB p.Glu501Asp (0.86), gyrA p.Ala90Val (0.13)
Ciprofloxacin R gyrB p.Glu501Asp (0.86), gyrA p.Ala90Val (0.13)
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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
lineage4.4.1.1.1 Euro-American S;Orphans None 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 6742 p.Glu501Asp missense_variant 0.86 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 0.13 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761277 p.Ile491Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 765639 p.Glu757Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779315 p.Arg109Leu missense_variant 0.18
mmpR5 779454 c.466dupC frameshift_variant 0.84
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
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087007 c.188_189insT frameshift_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326632 p.His281Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0