TB-Profiler result

Run: ERR2514739

Summary

Run ID: ERR2514739

Sample name:

Date: 20-10-2023 12:19:47

Number of reads: 1215982

Percentage reads mapped: 96.18

Strain: lineage4.8

Drug-resistance: Other


Download CSV Download TXT Download PDF Download JSON
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 (0.70)
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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 0.7 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
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 1472713 n.868T>C non_coding_transcript_exon_variant 0.65
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.65
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.74
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.74
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.64
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.54
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.5
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.38
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.46
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.46
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102055 p.Pro330Ser missense_variant 1.0
PPE35 2168076 p.Thr846Met missense_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
alr 3841256 c.165C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0