TB-Profiler result

Run: ERR4817977

Summary

Run ID: ERR4817977

Sample name:

Date: 20-10-2023 08:32:47

Number of reads: 4055772

Percentage reads mapped: 98.4

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 (0.26)
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 0.26 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
embR 1417298 p.Gly17Glu missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.47
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.47
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.23
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.29
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.27
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.26
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.34
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.31
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.52
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.26
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.32
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.3
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.26
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086739 c.-81G>A upstream_gene_variant 1.0
fbiA 3640689 p.Asp49Glu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246277 c.-237G>A upstream_gene_variant 1.0
embB 4247676 p.Ala388Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407945 c.258C>T synonymous_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0