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Detailed information for vg0321960786:

Variant ID: vg0321960786 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21960786
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, T: 0.02, G: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


TCCACTTTATGAATGGTGGCAGGAAATAACAAGATGATAAAAAAATCAATATACAAATATACTCTCTTTATTCTCAAATAGATTGTGTTTAGAATAATGT[A/T]
GTGCCACTGCTGGAGAAACCATCTTTGTTGGGTTCGCCAAAAACAACATTATTCCTGGTTCCAATAAGAACCGGGACTAAACATTATTTTTTTGTCCCGG

Reverse complement sequence

CCGGGACAAAAAAATAATGTTTAGTCCCGGTTCTTATTGGAACCAGGAATAATGTTGTTTTTGGCGAACCCAACAAAGATGGTTTCTCCAGCAGTGGCAC[T/A]
ACATTATTCTAAACACAATCTATTTGAGAATAAAGAGAGTATATTTGTATATTGATTTTTTTATCATCTTGTTATTTCCTGCCACCATTCATAAAGTGGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.90% 45.00% 0.11% 0.00% NA
All Indica  2759 90.30% 9.60% 0.11% 0.00% NA
All Japonica  1512 0.90% 99.10% 0.00% 0.00% NA
Aus  269 20.10% 79.90% 0.00% 0.00% NA
Indica I  595 91.10% 8.70% 0.17% 0.00% NA
Indica II  465 95.70% 4.30% 0.00% 0.00% NA
Indica III  913 91.70% 8.30% 0.00% 0.00% NA
Indica Intermediate  786 84.90% 14.90% 0.25% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 1.60% 98.40% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 37.80% 60.00% 2.22% 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
vg0321960786 A -> T LOC_Os03g39540.1 upstream_gene_variant ; 296.0bp to feature; MODIFIER silent_mutation Average:40.088; most accessible tissue: Minghui63 flag leaf, score: 60.569 N N N N
vg0321960786 A -> T LOC_Os03g39530.1 downstream_gene_variant ; 4329.0bp to feature; MODIFIER silent_mutation Average:40.088; most accessible tissue: Minghui63 flag leaf, score: 60.569 N N N N
vg0321960786 A -> T LOC_Os03g39550.1 downstream_gene_variant ; 2429.0bp to feature; MODIFIER silent_mutation Average:40.088; most accessible tissue: Minghui63 flag leaf, score: 60.569 N N N N
vg0321960786 A -> T LOC_Os03g39540-LOC_Os03g39550 intergenic_region ; MODIFIER silent_mutation Average:40.088; most accessible tissue: Minghui63 flag leaf, score: 60.569 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321960786 NA 8.71E-06 mr1718 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
vg0321960786 NA 2.00E-13 mr1750 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
vg0321960786 2.33E-06 NA mr1750_2 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
vg0321960786 1.34E-11 6.46E-25 mr1750_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