TB-Profiler result

Run: ERR4822200

Summary

Run ID: ERR4822200

Sample name:

Date: 20-10-2023 09:50:19

Number of reads: 2784025

Percentage reads mapped: 93.44

Strain: lineage4.3.4.1

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 (0.94)
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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 0.94 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 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G 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 1472108 n.263C>T non_coding_transcript_exon_variant 0.36
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.42
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.44
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.45
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.5
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.47
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.42
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.71
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.73
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.89
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.91
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.89
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.9
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.89
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.82
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.93
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.88
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.88
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.82
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.94
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.96
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.94
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.93
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.91
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.89
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.89
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.92
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.7
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.71
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.65
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.59
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.62
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.48
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.5
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.47
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039991 c.714G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0