TB-Profiler result

Run: ERR4828429
Summary

Run ID: ERR4828429

Sample name:

Date: 20-10-2023 13:57:27

Number of reads: 1733830

Percentage reads mapped: 99.58

Strain: lineage4.5;lineage2.2.1

Drug-resistance: Sensitive

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
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 0.56
lineage4 Euro-American LAM;T;S;X;H None 0.45
lineage4.5 Euro-American H;T RD122 0.41
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.55
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.56
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
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 7892 c.591G>A synonymous_variant 0.54
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.61
mshA 575907 p.Ala187Val missense_variant 0.57
ccsA 620029 c.139C>T synonymous_variant 0.44
ccsA 620625 p.Ile245Met missense_variant 0.61
rpoC 763031 c.-339T>C upstream_gene_variant 0.62
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.62
mmpL5 776182 p.Asp767Asn missense_variant 0.54
mmpL5 778950 c.-470C>T upstream_gene_variant 0.51
mmpS5 779615 c.-710C>G upstream_gene_variant 0.74
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303326 c.396C>T synonymous_variant 0.33
Rv1258c 1406760 c.580_581insC frameshift_variant 0.47
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.57
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.58
PPE35 2167926 p.Leu896Ser missense_variant 0.41
PPE35 2170568 p.Ile15Met missense_variant 0.45
Rv1979c 2222357 p.Thr270Ala missense_variant 0.51
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.65
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
Rv3236c 3612813 p.Thr102Ala missense_variant 0.58
clpC1 4038318 p.Pro796Leu missense_variant 0.47
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.5
embA 4243737 p.Gln169Glu missense_variant 0.6
aftB 4267647 p.Asp397Gly missense_variant 0.56
ethA 4328212 c.-740delC upstream_gene_variant 0.57
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.57
gid 4407927 p.Glu92Asp missense_variant 0.49