TB-Profiler result

Run: ERR1035316
Summary

Run ID: ERR1035316

Sample name:

Date: 20-10-2023 21:40:50

Number of reads: 4822851

Percentage reads mapped: 97.76

Strain: lineage4.3.2

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (1.00)
Isoniazid R katG p.Ser315Thr (0.97)
Ethambutol
Pyrazinamide R pncA p.His71Gln (1.00)
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 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
pncA 2289029 p.His71Gln missense_variant 1.0 pyrazinamide
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
rpoC 764995 c.1626C>G synonymous_variant 1.0
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 0.8
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.33
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.45
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.46
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.5
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.45
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.45
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.46
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.39
rrl 1473924 n.267_268insT non_coding_transcript_exon_variant 0.39
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.4
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.4
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.37
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.35
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.41
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.41
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.46
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.52
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.52
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.47
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.42
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.35
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.38
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.39
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.41
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.44
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.47
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169994 p.Leu207Val missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841441 c.-21C>A upstream_gene_variant 1.0
ddn 3986943 p.Gly34Arg missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0