TB-Profiler result

Run: ERR11488968
Summary

Run ID: ERR11488968

Sample name:

Date: 07-01-2024 02:11:29

Number of reads: 3537319

Percentage reads mapped: 99.52

Strain: lineage4.4.1.1.1;lineage4.3.4.1

Drug-resistance: MDR-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 R rpoB p.Ser450Leu (0.17)
Isoniazid R katG p.Ser315Thr (0.11)
Ethambutol R embB p.Met306Ile (0.13)
Pyrazinamide R pncA p.Tyr34Asp (0.12)
Streptomycin R rpsL p.Lys43Arg (0.12)
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 0.87
lineage4.4 Euro-American S;T None 0.15
lineage4.4.1 Euro-American (S-type) S;T None 0.14
lineage4.3.4 Euro-American (LAM) LAM RD174 0.87
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.86
lineage4.4.1.1 Euro-American S;Orphans None 0.16
lineage4.4.1.1.1 Euro-American S;Orphans None 0.15
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 761155 p.Ser450Leu missense_variant 0.17 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.12 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.11 isoniazid
pncA 2289142 p.Tyr34Asp missense_variant 0.12 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.13 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
rpoC 764995 c.1626C>G synonymous_variant 0.82
rpoC 766487 p.Pro1040Ser missense_variant 0.12
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 2102990 p.Val18Ala missense_variant 0.11
PPE35 2169840 p.Gly258Asp missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064993 p.Trp400* stop_gained 0.17
thyA 3073868 p.Thr202Ala missense_variant 0.82
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.87
Rv3236c 3612665 p.Val151Ala missense_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 0.81
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269308 p.Phe176Leu missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.83
gid 4408330 c.-128G>C upstream_gene_variant 0.77