TB-Profiler result

Run: ERR4821924
Summary

Run ID: ERR4821924

Sample name:

Date: 20-10-2023 09:45:57

Number of reads: 5701502

Percentage reads mapped: 98.17

Strain: lineage4.6.2.2

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol
Pyrazinamide
Streptomycin R rrs n.888G>A (0.84)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00)
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
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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 0.84 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.66
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.71
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.72
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.72
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.77
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.81
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.44
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.39
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.44
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.88
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.81
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.81
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.53
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.25
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.75
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.76
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.86
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.86
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.88
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.84
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.78
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.38
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.38
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.33
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.24
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155389 c.723C>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067474 p.Pro158Ala missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612910 p.Leu69Phe missense_variant 1.0
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0