TB-Profiler result

Run: ERR4811239
Summary

Run ID: ERR4811239

Sample name:

Date: 20-10-2023 15:18:05

Number of reads: 10158724

Percentage reads mapped: 99.47

Strain: lineage2.2.1

Drug-resistance: RR-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 (1.00)
Isoniazid
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Lys96Glu (0.12), pncA p.Thr47Ala (0.15), pncA p.Ile6Thr (0.16), pncA c.-11A>G (0.23)
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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
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 1.0 rifampicin
pncA 2288956 p.Lys96Glu missense_variant 0.12 pyrazinamide
pncA 2289103 p.Thr47Ala missense_variant 0.15 pyrazinamide
pncA 2289225 p.Ile6Thr missense_variant 0.16 pyrazinamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.23 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 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
gyrB 6401 p.Cys388Gly missense_variant 1.0
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 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764666 p.Gly433Ser missense_variant 1.0
rpoC 765178 c.1809C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673217 c.-223A>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155819 p.Tyr98Cys missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878641 c.-135delG upstream_gene_variant 1.0
embC 4242232 c.2370T>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243263 p.Arg11Trp missense_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269124 p.Ala237Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 0.49
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0