TB-Profiler result

Run: ERR4799793

Summary

Run ID: ERR4799793

Sample name:

Date: 20-10-2023 03:13:28

Number of reads: 3542073

Percentage reads mapped: 99.36

Strain: lineage4.2.2.2

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 (0.98)
Isoniazid R fabG1 c.-15C>T (0.91), katG p.Ser315Thr (0.98)
Ethambutol R embB p.Met306Val (0.94)
Pyrazinamide R pncA p.His51Arg (0.96)
Streptomycin R rpsL p.Lys88Arg (0.98)
Fluoroquinolones R gyrA p.Ala90Val (0.96)
Moxifloxacin R gyrA p.Ala90Val (0.96)
Ofloxacin R gyrA p.Ala90Val (0.96)
Levofloxacin R gyrA p.Ala90Val (0.96)
Ciprofloxacin R gyrA p.Ala90Val (0.96)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.91)
Clofazimine
Para-aminosalicylic_acid R folC p.Glu153Ala (0.98)
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 0.99
lineage4.2 Euro-American H;T;LAM None 0.97
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.97
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 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 7570 p.Ala90Val missense_variant 0.96 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.98 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.91 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2289090 p.His51Arg missense_variant 0.96 pyrazinamide
folC 2747141 p.Glu153Ala missense_variant 0.98 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.94 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 8688 p.Ala463Ser missense_variant 0.91
gyrA 9304 p.Gly668Asp missense_variant 0.99
mshA 576077 c.730C>T synonymous_variant 0.92
rpoB 761293 p.Val496Ala missense_variant 0.98
rpoB 761489 c.1683G>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779101 p.Arg38* stop_gained 0.97
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 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289433 c.-192C>T upstream_gene_variant 0.98
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.91
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 0.98
embB 4246725 p.Leu71Pro missense_variant 0.97
ubiA 4269148 p.Val229Ala missense_variant 0.92
whiB6 4338382 p.Asp47Gly missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0