TB-Profiler result

Run: ERR108465

Summary

Run ID: ERR108465

Sample name:

Date: 21-10-2023 05:59:11

Number of reads: 6584342

Percentage reads mapped: 99.56

Strain: lineage4.2.1;lineage4.1.2

Drug-resistance: HR-TB


Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (0.18)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.13)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethR p.Phe110Leu (0.84)
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 0.8
lineage4.2 Euro-American H;T;LAM None 0.18
lineage4.1.2 Euro-American T;H None 0.8
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.18
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 0.13 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.18 isoniazid
ethR 4327876 p.Phe110Leu missense_variant 0.84 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 0.84
rpoB 760115 c.309C>T synonymous_variant 0.84
rpoC 765150 p.Gly594Glu missense_variant 0.83
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800889 c.81C>A synonymous_variant 0.83
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168303 c.2310G>T synonymous_variant 0.79
PPE35 2169776 p.Phe279Leu missense_variant 0.82
PPE35 2169879 p.Phe245Cys missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.84
ald 3086742 c.-78A>C upstream_gene_variant 0.17
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 0.85
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.8
embB 4247086 c.573C>T synonymous_variant 0.83
embB 4249594 c.3081G>A synonymous_variant 0.14
ubiA 4269847 c.-14A>G upstream_gene_variant 0.81
ethA 4328376 c.-903G>C upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0