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Detailed information for vg0306928785:

Variant ID: vg0306928785 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 6928785
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


CTTAGAGTTTGTTAGAGATAATAGTCGTGTCCGATATGGACATATCTTGTAATTTTCGGGTATAAATAGACCCGAACCCTATGTAATCAAACTAACACAC[G/A]
TTCAATATAATCTCGGCGCATCGCCACCCTTTTTGCTTTCGTTTTATTTCGACGAGTTCTTACTTTCGGGTTGAGCTGCATCGGTTTCGATCTTCAACAA

Reverse complement sequence

TTGTTGAAGATCGAAACCGATGCAGCTCAACCCGAAAGTAAGAACTCGTCGAAATAAAACGAAAGCAAAAAGGGTGGCGATGCGCCGAGATTATATTGAA[C/T]
GTGTGTTAGTTTGATTACATAGGGTTCGGGTCTATTTATACCCGAAAATTACAAGATATGTCCATATCGGACACGACTATTATCTCTAACAAACTCTAAG

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 98.30% 1.20% 0.49% 0.00% NA
All Indica  2759 97.00% 2.10% 0.83% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.60% 5.20% 2.18% 0.00% NA
Indica II  465 98.10% 1.10% 0.86% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 96.30% 2.90% 0.76% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% 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
vg0306928785 G -> A LOC_Os03g12860.1 upstream_gene_variant ; 2924.0bp to feature; MODIFIER silent_mutation Average:36.585; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0306928785 G -> A LOC_Os03g12850-LOC_Os03g12860 intergenic_region ; MODIFIER silent_mutation Average:36.585; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0306928785 NA 2.52E-06 mr1060_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
vg0306928785 3.41E-06 1.40E-06 mr1265_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
vg0306928785 NA 2.51E-06 mr1380_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
vg0306928785 NA 8.62E-07 mr1576_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
vg0306928785 6.66E-06 NA mr1709_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