TB-Profiler result

Run: ERR4819790
Summary

Run ID: ERR4819790

Sample name:

Date: 20-10-2023 09:02:51

Number of reads: 4407008

Percentage reads mapped: 98.9

Strain: lineage4.6

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 (0.44)
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
lineage4.6 Euro-American T;LAM None 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 0.44 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8266 p.Ala322Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491349 c.567T>C synonymous_variant 1.0
rpoC 766586 p.Glu1073Lys missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775822 p.Val887Met missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303098 c.168C>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.43
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.45
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.45
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.43
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.43
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.44
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.44
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.55
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.5
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.55
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.53
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.5
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.31
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.26
rrs 1473318 n.1473G>A non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156267 c.-156A>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G 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
ethA 4328462 c.-989C>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407554 p.Arg217Trp missense_variant 1.0