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Detailed information for vg0203225917:

Variant ID: vg0203225917 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 3225917
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: Unkown

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


GGAGGATGCCTCGCATTGTGATTAATCTGGGGAGTACTACACTTGCAAAAAGCTAATTAGGATTTAATTAATTAGTTGATTAATTAGGTAATTAATGACC[A/C]
TCTCGGCGAGGCTATGGCTATCGGTGGCTTGTCCCATCCTCGCCCTCACATGGATGTAGTCTTTGGCTGGCTCTGGCTTCTCCTCAGCTGCCGCCGCGTC

Reverse complement sequence

GACGCGGCGGCAGCTGAGGAGAAGCCAGAGCCAGCCAAAGACTACATCCATGTGAGGGCGAGGATGGGACAAGCCACCGATAGCCATAGCCTCGCCGAGA[T/G]
GGTCATTAATTACCTAATTAATCAACTAATTAATTAAATCCTAATTAGCTTTTTGCAAGTGTAGTACTCCCCAGATTAATCACAATGCGAGGCATCCTCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of Unkown(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.00% 0.00% 1.42% 7.62% NA
All Indica  2759 87.70% 0.00% 1.74% 10.58% NA
All Japonica  1512 94.70% 0.00% 1.12% 4.17% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.30% 0.00% 0.17% 3.53% NA
Indica II  465 81.10% 0.00% 2.58% 16.34% NA
Indica III  913 83.80% 0.00% 2.41% 13.80% NA
Indica Intermediate  786 89.60% 0.00% 1.65% 8.78% NA
Temperate Japonica  767 96.50% 0.00% 0.78% 2.74% NA
Tropical Japonica  504 91.90% 0.00% 1.79% 6.35% NA
Japonica Intermediate  241 95.00% 0.00% 0.83% 4.15% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 0.00% 2.22% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0203225917 A -> C LOC_Os02g06460.1 upstream_gene_variant ; 726.0bp to feature; MODIFIER N Average:69.389; most accessible tissue: Minghui63 panicle, score: 86.012 N N N N
vg0203225917 A -> C LOC_Os02g06470.1 upstream_gene_variant ; 1591.0bp to feature; MODIFIER N Average:69.389; most accessible tissue: Minghui63 panicle, score: 86.012 N N N N
vg0203225917 A -> C LOC_Os02g06480.1 downstream_gene_variant ; 1591.0bp to feature; MODIFIER N Average:69.389; most accessible tissue: Minghui63 panicle, score: 86.012 N N N N
vg0203225917 A -> C LOC_Os02g06480.2 downstream_gene_variant ; 1591.0bp to feature; MODIFIER N Average:69.389; most accessible tissue: Minghui63 panicle, score: 86.012 N N N N
vg0203225917 A -> C LOC_Os02g06460-LOC_Os02g06470 intergenic_region ; MODIFIER N Average:69.389; most accessible tissue: Minghui63 panicle, score: 86.012 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0203225917 6.53E-06 NA mr1721_2 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
vg0203225917 7.85E-06 7.85E-06 mr1853_2 Ind_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