TB-Profiler result

Run: ERR3335777
Summary

Run ID: ERR3335777

Sample name:

Date: 21-10-2023 15:18:58

Number of reads: 7051791

Percentage reads mapped: 99.43

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 p.Ser450Leu (0.77)
Isoniazid R katG p.Ser315Thr (0.74)
Ethambutol R embB p.Met306Leu (0.82)
Pyrazinamide
Streptomycin R gid p.Ala80Pro (0.71)
Fluoroquinolones R gyrA p.Ser91Pro (0.75)
Moxifloxacin R gyrA p.Ser91Pro (0.75)
Ofloxacin R gyrA p.Ser91Pro (0.75)
Levofloxacin R gyrA p.Ser91Pro (0.75)
Ciprofloxacin R gyrA p.Ser91Pro (0.75)
Aminoglycosides R rrs n.1401A>G (0.77)
Amikacin R rrs n.1401A>G (0.77)
Capreomycin R rrs n.1401A>G (0.77)
Kanamycin R rrs n.1401A>G (0.77)
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
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 7572 p.Ser91Pro missense_variant 0.75 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.77 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.77 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.74 isoniazid
embB 4247429 p.Met306Leu missense_variant 0.82 ethambutol
gid 4407965 p.Ala80Pro missense_variant 0.71 streptomycin
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 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766740 p.Val1124Gly missense_variant 0.66
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781879 p.Val107Ala missense_variant 0.82
Rv1258c 1406369 c.972G>T synonymous_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918461 c.522C>T synonymous_variant 0.74
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 0.98
ahpC 2726107 c.-86T>G upstream_gene_variant 0.76
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 0.24
clpC1 4039940 c.765G>A synonymous_variant 0.82
clpC1 4040153 p.Glu184Asp missense_variant 0.76
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