TB-Profiler result

Run: ERR4821139

Summary

Run ID: ERR4821139

Sample name:

Date: 20-10-2023 09:33:17

Number of reads: 2928881

Percentage reads mapped: 97.11

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 (0.68)
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 0.68 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 7617 p.Arg106Cys 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 0.29
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.44
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.57
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.68
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.68
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.71
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.69
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.73
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.82
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.59
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.62
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.62
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.62
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.71
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.71
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.77
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.69
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.67
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.64
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.64
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
alr 3840764 c.657G>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244374 p.Pro381Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338599 c.-78A>C upstream_gene_variant 1.0
gid 4407683 p.His174Asp missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0