TB-Profiler result

Run: ERR4814699

Summary

Run ID: ERR4814699

Sample name:

Date: 20-10-2023 07:37:18

Number of reads: 3349200

Percentage reads mapped: 97.16

Strain: lineage4.1.2.1

Drug-resistance: HR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00)
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.69
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.38
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.61
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.57
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.67
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.44
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.74
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.78
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.37
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.38
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.79
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.8
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.61
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.35
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.67
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.68
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.67
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.53
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.69
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
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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0