TB-Profiler result

Run: SRR5067671
Summary

Run ID: SRR5067671

Sample name:

Date: 21-10-2023 04:24:03

Number of reads: 1473709

Percentage reads mapped: 99.54

Strain: lineage4.1.2.1;lineage2.2

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 (1.00)
Ethambutol
Pyrazinamide R pncA p.Lys96Gln (0.93)
Streptomycin R rpsL p.Lys43Arg (1.00)
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 0.98
lineage4.1 Euro-American T;X;H None 0.95
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.06
lineage4.1.2 Euro-American T;H None 0.95
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.92
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288956 p.Lys96Gln missense_variant 0.93 pyrazinamide
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 0.95
mshA 575679 p.Asn111Ser missense_variant 0.94
rpoB 760115 c.309C>T synonymous_variant 0.97
rpoC 763031 c.-339T>G upstream_gene_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 0.96
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406824 p.Thr173Pro missense_variant 0.93
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471766 n.-80G>A upstream_gene_variant 0.93
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.96
eis 2714673 c.660C>T synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.94
aftB 4267798 c.1039C>T synonymous_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0