TB-Profiler result

Run: ERR7363028

Summary

Run ID: ERR7363028

Sample name:

Date: 20-05-2023 23:30:00

Number of reads: 5339348

Percentage reads mapped: 99.59

Strain: lineage4.3.2;lineage4.1.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 0.21
lineage4.1 Euro-American T;X;H None 0.8
lineage4.3.2 Euro-American (LAM) LAM3 None 0.22
lineage4.1.2 Euro-American T;H None 0.76
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.78
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.81
mshA 575679 p.Asn111Ser missense_variant 0.79
mshA 576482 p.Val379Leu missense_variant 0.11
rpoB 760115 c.309C>T synonymous_variant 0.83
rpoC 764995 c.1626C>G synonymous_variant 0.2
rpoC 765150 p.Gly594Glu missense_variant 0.8
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.24
rrs 1472646 n.801C>T non_coding_transcript_exon_variant 0.72
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.81
kasA 2519131 c.1017G>T synonymous_variant 0.21
thyA 3073868 p.Thr202Ala missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640838 p.Pro99Arg missense_variant 0.77
ddn 3986910 p.Arg23Trp missense_variant 0.23
clpC1 4038287 c.2418C>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.77
embB 4246584 p.Arg24Pro missense_variant 0.28
embB 4248914 p.Ala801Thr missense_variant 0.24
ubiA 4269974 c.-141C>G upstream_gene_variant 0.39
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.2