TB-Profiler result

Run: ERR4817309
Summary

Run ID: ERR4817309

Sample name:

Date: 20-10-2023 08:21:24

Number of reads: 2260331

Percentage reads mapped: 93.6

Strain: lineage4.5

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 (0.70)
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
lineage4.5 Euro-American H;T RD122 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9788 p.Asp829Glu missense_variant 1.0
ccsA 620029 c.139C>T synonymous_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 0.64
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.53
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.64
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.68
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.65
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.8
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.83
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.3
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.53
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.32
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.9
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.9
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.55
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.67
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.67
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.16
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.69
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.28
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.64
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.63
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.47
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.35
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.35
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.62
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.5
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.62
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.54
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.44
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.67
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.77
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.7
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.7
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.65
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.71
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.63
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.58
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.71
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.78
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.7
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.64
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170394 c.219G>A synonymous_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2221722 c.1443C>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0