TB-Profiler result

Run: ERR4831483
Summary

Run ID: ERR4831483

Sample name:

Date: 20-10-2023 15:34:48

Number of reads: 3176610

Percentage reads mapped: 99.68

Strain: lineage3

Drug-resistance: Pre-XDR-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 c.1312_1314delAAC (0.15), rpoB p.Ser450Leu (0.83)
Isoniazid R katG c.152delA (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA c.463_465dupGTG (0.24), pncA p.Val139Ala (0.14), pncA p.Tyr103His (0.53)
Streptomycin
Fluoroquinolones R gyrA p.Asp94His (1.00)
Moxifloxacin R gyrA p.Asp94His (1.00)
Ofloxacin R gyrA p.Asp94His (1.00)
Levofloxacin R gyrA p.Asp94His (1.00)
Ciprofloxacin R gyrA p.Asp94His (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.851delC (0.23), ethA c.851delC (0.23), ethA c.695_696dupCC (0.22), ethA c.578dupC (0.15), ethA c.578dupC (0.15)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 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
gyrA 7581 p.Asp94His missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761114 c.1312_1314delAAC conservative_inframe_deletion 0.15 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.83 rifampicin
katG 2155959 c.152delA frameshift_variant 1.0 isoniazid
pncA 2288776 c.463_465dupGTG conservative_inframe_insertion 0.24 pyrazinamide
pncA 2288826 p.Val139Ala missense_variant 0.14 pyrazinamide
pncA 2288935 p.Tyr103His missense_variant 0.53 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326622 c.851delC frameshift_variant 0.23 ethionamide, ethionamide
ethA 4326777 c.695_696dupCC frameshift_variant 0.22 ethionamide
ethA 4326895 c.578dupC frameshift_variant 0.15 ethionamide, 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 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777484 p.Gln333Glu missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167679 c.2934G>C synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289636 c.-395A>C upstream_gene_variant 0.97
ahpC 2726105 c.-88G>A 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
fbiB 3642877 p.Lys448Arg missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0