TB-Profiler result

Run: ERR4816681

Summary

Run ID: ERR4816681

Sample name:

Date: 20-10-2023 08:10:15

Number of reads: 4131423

Percentage reads mapped: 95.27

Strain: lineage4.1.2.1

Drug-resistance: Other


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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 R rrs n.888G>A (0.71), gid c.351delG (1.00)
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.71 streptomycin
gid 4407851 c.351delG frameshift_variant 1.0 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 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407489 c.-149G>A upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.77
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.84
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.81
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.83
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.82
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.84
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.8
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.88
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.85
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.85
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.7
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.53
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.63
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.65
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.7
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.7
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.72
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.67
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.68
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.23
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
Rv2752c 3066299 c.-108C>T upstream_gene_variant 1.0
thyX 3067910 c.36C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244014 p.Leu261Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0