TB-Profiler result

Run: ERR11049295
Summary

Run ID: ERR11049295

Sample name:

Date: 2024-10-05T03:54:58.136078

Number of reads: 2999997

Percentage reads mapped: 99.75

Median coverage: 99.5

Strain: lineage4.1;lineage4.3.3

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.76
lineage4.1 Euro-American None 0.23
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.78
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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 Confidence Comment
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 Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.3 isoniazid
ethionamide
Rv0565c 657269 p.Ser68Pro missense_variant 0.24 ethionamide Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.8 rifampicin Not assoc w R
rpoC 765012 p.Ser548Thr missense_variant 0.19 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 0.21 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.26 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.76 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063334 c.1395C>T synonymous_variant 0.31 kanamycin
capreomycin
streptomycin
amikacin
katG 2156196 c.-85C>T upstream_gene_variant 0.78 isoniazid Not assoc w R
PPE35 2168051 c.2562G>A synonymous_variant 0.2 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 0.79 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.83 para-aminosalicylic_acid
ribD 2986875 p.Pro13Ser missense_variant 0.27 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.82 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.74 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.78 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.22 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.3 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.81 streptomycin Not assoc w R