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Detailed information for vg0432358320:

Variant ID: vg0432358320 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32358320
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTGTCATCAAATGTTCTTAAGCATGACATAAATATTTTCATATTTGCACAAAAATTTTGAATAAAACGAATGGTCAAACGTTGGTCGAAAAGTCAACG[G/A]
CGTCATACATTAAAATACGGAGGGAATATTAATATGCACAGGGATACCGAGTACACATTCACATTCTCCGGGAGTACAGCTTCTAGCCTCTTAGGGGAGC

Reverse complement sequence

GCTCCCCTAAGAGGCTAGAAGCTGTACTCCCGGAGAATGTGAATGTGTACTCGGTATCCCTGTGCATATTAATATTCCCTCCGTATTTTAATGTATGACG[C/T]
CGTTGACTTTTCGACCAACGTTTGACCATTCGTTTTATTCAAAATTTTTGTGCAAATATGAAAATATTTATGTCATGCTTAAGAACATTTGATGACAAAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.40% 2.60% 0.02% 0.00% NA
All Indica  2759 98.20% 1.80% 0.04% 0.00% NA
All Japonica  1512 95.60% 4.40% 0.00% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 96.40% 3.50% 0.11% 0.00% NA
Indica Intermediate  786 98.60% 1.40% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 87.10% 12.90% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0432358320 G -> A LOC_Os04g54390.1 upstream_gene_variant ; 4648.0bp to feature; MODIFIER silent_mutation Average:59.158; most accessible tissue: Callus, score: 82.299 N N N N
vg0432358320 G -> A LOC_Os04g54360.1 downstream_gene_variant ; 2277.0bp to feature; MODIFIER silent_mutation Average:59.158; most accessible tissue: Callus, score: 82.299 N N N N
vg0432358320 G -> A LOC_Os04g54380.1 downstream_gene_variant ; 882.0bp to feature; MODIFIER silent_mutation Average:59.158; most accessible tissue: Callus, score: 82.299 N N N N
vg0432358320 G -> A LOC_Os04g54370.1 intron_variant ; MODIFIER silent_mutation Average:59.158; most accessible tissue: Callus, score: 82.299 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432358320 NA 9.87E-07 mr1040_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0432358320 NA 3.01E-06 mr1243_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0432358320 NA 6.46E-06 mr1253_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0432358320 3.52E-07 2.25E-08 mr1255_2 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0432358320 NA 2.82E-08 mr1800_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251