Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0207732987:

Variant ID: vg0207732987 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 7732987
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


AACCAATCGTGGAAATGATATATCCTACTAGCAAAGGACACGTGGATCATCCAAAACGATCCAACTTATTCCATCGAAGTGCTCAAACTTCTCCATTACC[G/A]
TCACCAAACTCACCTCCAAAGCCACTACTACCATCAAATCCACCATTGAGGGCAGCCACCTTTGAAGCTGCAATTTGTGTCCTCATAGCCAACACATATG

Reverse complement sequence

CATATGTGTTGGCTATGAGGACACAAATTGCAGCTTCAAAGGTGGCTGCCCTCAATGGTGGATTTGATGGTAGTAGTGGCTTTGGAGGTGAGTTTGGTGA[C/T]
GGTAATGGAGAAGTTTGAGCACTTCGATGGAATAAGTTGGATCGTTTTGGATGATCCACGTGTCCTTTGCTAGTAGGATATATCATTTCCACGATTGGTT

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 87.30% 12.00% 0.68% 0.00% NA
All Indica  2759 89.60% 9.30% 1.12% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 14.90% 85.10% 0.00% 0.00% NA
Indica I  595 79.70% 17.50% 2.86% 0.00% NA
Indica II  465 94.60% 4.90% 0.43% 0.00% NA
Indica III  913 95.40% 4.60% 0.00% 0.00% NA
Indica Intermediate  786 87.30% 11.20% 1.53% 0.00% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 41.70% 58.30% 0.00% 0.00% NA
Intermediate  90 80.00% 18.90% 1.11% 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
vg0207732987 G -> A LOC_Os02g14140.1 downstream_gene_variant ; 285.0bp to feature; MODIFIER silent_mutation Average:19.274; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N
vg0207732987 G -> A LOC_Os02g14130-LOC_Os02g14140 intergenic_region ; MODIFIER silent_mutation Average:19.274; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0207732987 1.84E-10 1.97E-16 mr1570 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
vg0207732987 3.20E-07 1.00E-06 mr1570 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
vg0207732987 4.89E-08 1.11E-07 mr1570_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