TB-Profiler result

Run: SRR26400038
Summary

Run ID: SRR26400038

Sample name:

Date: 05-02-2024 21:09:16

Number of reads: 3308197

Percentage reads mapped: 99.52

Strain: lineage4.1.2

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (0.95)
Ethambutol
Pyrazinamide
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
lineage4.1 Euro-American T;X;H None 0.96
lineage4.1.2 Euro-American T;H None 0.98
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
katG 2155168 p.Ser315Thr missense_variant 0.95 isoniazid
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 490892 p.Val37Gly missense_variant 0.98
rpoC 765150 p.Gly594Glu missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417140 p.Ala70Ser missense_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673249 c.-191C>T upstream_gene_variant 0.96
tlyA 1917972 c.33A>G synonymous_variant 0.99
PPE35 2169202 p.Ser471Ala missense_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747022 p.Val193Ile missense_variant 0.94
Rv2752c 3065377 p.Val272Ala missense_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449642 p.Asn380Ser missense_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641164 p.Ile208Val missense_variant 1.0
ddn 3986755 c.-89G>C upstream_gene_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.95
ethA 4327265 p.Thr70Ser missense_variant 0.96
ethR 4327628 c.80_81delTGinsC frameshift_variant&missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0