TB-Profiler result

Run: ERR228053

Summary

Run ID: ERR228053

Sample name:

Date: 20-10-2023 15:12:47

Number of reads: 3373744

Percentage reads mapped: 99.61

Strain: lineage4.1.2

Drug-resistance: Other


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethR p.Phe110Leu (0.96)
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 0.94
lineage4.1 Euro-American T;X;H None 0.9
lineage4.1.2 Euro-American T;H None 0.91
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
ethR 4327876 p.Phe110Leu missense_variant 0.96 ethionamide
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
fgd1 491591 p.Lys270Met missense_variant 0.94
rpoB 759841 p.Ser12Thr missense_variant 0.89
rpoB 760115 c.309C>T synonymous_variant 0.97
rpoC 763031 c.-339T>C upstream_gene_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 0.85
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800889 c.81C>A synonymous_variant 0.95
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.14
PPE35 2168303 c.2310G>T synonymous_variant 0.9
PPE35 2169776 p.Phe279Leu missense_variant 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.92
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840263 c.1158C>T synonymous_variant 0.9
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.88
embB 4247086 c.573C>T synonymous_variant 0.88
ubiA 4269847 c.-14A>G upstream_gene_variant 0.84
whiB6 4338595 c.-75delG upstream_gene_variant 1.0