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Detailed information for vg0215252496:

Variant ID: vg0215252496 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 15252496
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTACAATCATTAGTAGCATGAGAAAAAGAATGATGCCATTTACAATAAGCCTTTCTACCCAGCTCTTCGGCTGACAGAATCACATGTCCCTCTCTGTCA[G/A]
TCTAATTTGTTTGCCTTGCAACAGTGTATCAAAAATTTTATCACATTTACTAACATCAAAAGTATACTTCATTTCTCCTCTTTTAGTAGGTGCAGGTTTC

Reverse complement sequence

GAAACCTGCACCTACTAAAAGAGGAGAAATGAAGTATACTTTTGATGTTAGTAAATGTGATAAAATTTTTGATACACTGTTGCAAGGCAAACAAATTAGA[C/T]
TGACAGAGAGGGACATGTGATTCTGTCAGCCGAAGAGCTGGGTAGAAAGGCTTATTGTAAATGGCATCATTCTTTTTCTCATGCTACTAATGATTGTAAT

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 91.80% 0.70% 4.42% 3.13% NA
All Indica  2759 86.90% 1.10% 7.47% 4.53% NA
All Japonica  1512 98.30% 0.00% 0.20% 1.52% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 91.30% 0.20% 4.87% 3.70% NA
Indica II  465 97.60% 0.40% 1.72% 0.22% NA
Indica III  913 76.20% 2.10% 12.81% 8.87% NA
Indica Intermediate  786 89.60% 1.10% 6.62% 2.67% NA
Temperate Japonica  767 96.60% 0.00% 0.39% 3.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0215252496 G -> A LOC_Os02g25980.1 downstream_gene_variant ; 4526.0bp to feature; MODIFIER silent_mutation Average:24.532; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg0215252496 G -> A LOC_Os02g25970.1 intron_variant ; MODIFIER silent_mutation Average:24.532; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg0215252496 G -> DEL N N silent_mutation Average:24.532; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0215252496 2.91E-06 2.91E-06 mr1591 Ind_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
vg0215252496 2.26E-08 2.26E-08 mr1890 Ind_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
vg0215252496 4.36E-06 4.36E-06 mr1891 Ind_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