TB-Profiler result

Run: ERR4813464

Summary

Run ID: ERR4813464

Sample name:

Date: 20-10-2023 05:00:58

Number of reads: 2328794

Percentage reads mapped: 99.83

Strain: lineage4.3.4.2;lineage4.3.3

Drug-resistance: MDR-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.Asp435Val (0.16), rpoB p.Ser450Leu (0.80)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (0.83), embB p.Tyr319Ser (0.15)
Pyrazinamide R pncA c.375_389delCGATGAGGTCGATGT (0.89), pncA p.Gln10Arg (0.19)
Streptomycin R gid p.Pro84Leu (0.14)
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 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.17
lineage4.3.4 Euro-American (LAM) LAM RD174 0.84
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.87
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 761110 p.Asp435Val missense_variant 0.16 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.8 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288852 c.375_389delCGATGAGGTCGATGT disruptive_inframe_deletion 0.89 pyrazinamide
pncA 2289213 p.Gln10Arg missense_variant 0.19 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.83 ethambutol
embB 4247469 p.Tyr319Ser missense_variant 0.15 ethambutol
gid 4407952 p.Pro84Leu missense_variant 0.14 streptomycin
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
gyrB 6140 p.Val301Leu missense_variant 0.88
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764918 p.Val517Leu missense_variant 0.9
rpoC 764995 c.1626C>G synonymous_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
rpsA 1833469 c.-73G>T upstream_gene_variant 0.88
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168998 p.Ile539Val missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.86
alr 3840719 c.702A>G synonymous_variant 0.81
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407970 p.Pro78Leu missense_variant 0.87
gid 4408156 p.Leu16Arg missense_variant 1.0