TB-Profiler result

Run: ERR4821283
Summary

Run ID: ERR4821283

Sample name:

Date: 20-10-2023 09:35:50

Number of reads: 2979270

Percentage reads mapped: 99.6

Strain: lineage4.1.2.1;lineage3

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
lineage3 East-African-Indian CAS RD750 0.74
lineage4 Euro-American LAM;T;S;X;H None 0.26
lineage4.1 Euro-American T;X;H None 0.24
lineage4.1.2 Euro-American T;H None 0.24
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.24
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 8948 c.1647G>A synonymous_variant 0.74
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.23
fgd1 491742 c.960T>C synonymous_variant 0.82
mshA 575679 p.Asn111Ser missense_variant 0.25
ccsA 620281 p.Arg131Cys missense_variant 0.84
rpoB 759746 c.-61C>T upstream_gene_variant 0.64
rpoB 760115 c.309C>T synonymous_variant 0.22
rpoB 760375 p.Asp190Ala missense_variant 0.33
rpoC 762434 c.-936T>G upstream_gene_variant 0.84
rpoC 763031 c.-339T>C upstream_gene_variant 0.75
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.75
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.79
PPE35 2167926 p.Leu896Ser missense_variant 0.73
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.79
pncA 2289083 c.159C>T synonymous_variant 0.17
pncA 2289365 c.-125delC upstream_gene_variant 0.7
kasA 2518076 c.-39C>T upstream_gene_variant 0.28
ahpC 2726105 c.-88G>A upstream_gene_variant 0.74
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 0.75
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.73
gid 4407866 c.336delT frameshift_variant 0.82