TB-Profiler result

Run: ERR4821519

Summary

Run ID: ERR4821519

Sample name:

Date: 20-10-2023 09:39:27

Number of reads: 3967465

Percentage reads mapped: 90.71

Strain: lineage3

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 (0.55)
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
lineage3 East-African-Indian CAS RD750 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 0.55 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 8164 p.Ala288Asp missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile 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 1471923 n.78T>C non_coding_transcript_exon_variant 0.27
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.24
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.43
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.26
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.41
rrs 1472431 n.586G>A non_coding_transcript_exon_variant 0.5
rrs 1472435 n.590T>C non_coding_transcript_exon_variant 0.5
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.67
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.92
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.36
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.5
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.56
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.46
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.5
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.33
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.5
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.43
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.68
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.67
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.38
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.59
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.5
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.26
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.35
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.45
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.5
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.44
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.44
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.55
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.55
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.47
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.54
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.59
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.6
rrl 1476524 n.2867_2868delCAinsT non_coding_transcript_exon_variant 0.52
rrl 1476535 n.2878G>A non_coding_transcript_exon_variant 0.52
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.52
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.48
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086960 c.141C>T synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4240073 p.Glu71Lys missense_variant 0.99
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0