TB-Profiler result

Run: ERR4816758

Summary

Run ID: ERR4816758

Sample name:

Date: 20-10-2023 08:11:32

Number of reads: 4063925

Percentage reads mapped: 96.84

Strain: lineage4.8

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 (0.39)
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 0.39 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
mshA 575891 p.Ala182Thr missense_variant 1.0
rpoB 762667 p.Pro954Arg 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 1472530 n.685G>A non_coding_transcript_exon_variant 0.44
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.54
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.65
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.65
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.64
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.64
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.62
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.42
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.37
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.44
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.36
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.39
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.5
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.5
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.4
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.38
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.32
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.28
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.38
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 0.25
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.43
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.32
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.53
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.47
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.47
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.5
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.5
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.62
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.54
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.67
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.62
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.62
rrl 1474753 n.1096_1097delACinsG non_coding_transcript_exon_variant 0.43
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.43
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.67
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.73
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.75
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.75
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.89
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.75
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.6
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242928 c.-305A>G upstream_gene_variant 1.0
embB 4247595 p.Cys361Ser missense_variant 1.0
aftB 4268040 p.Leu266Pro missense_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