TB-Profiler result

Run: ERR2707071

Summary

Run ID: ERR2707071

Sample name:

Date: 19-10-2023 12:00:16

Number of reads: 2467543

Percentage reads mapped: 99.72

Strain: lineage4.3.4.1

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.His445Asp (0.97)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00), embB p.Gly406Ser (1.00)
Pyrazinamide R pncA c.316_319dupTTCG (0.33), pncA p.Tyr103* (0.30)
Streptomycin
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 0.99
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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
rpoB 761139 p.His445Asp missense_variant 0.97 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288922 c.316_319dupTTCG frameshift_variant 0.33 pyrazinamide
pncA 2288933 p.Tyr103* stop_gained 0.3 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4247729 p.Gly406Ser 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
rpoB 763021 p.Ala1072Gly missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.99
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
ndh 2102919 c.124C>T synonymous_variant 1.0
PPE35 2168008 p.Ile869Val missense_variant 1.0
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288844 p.Ile133Ser missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 0.99
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 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039991 c.714G>A synonymous_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407902 p.Leu101Val missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.99