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Detailed information for vg0828307900:

Variant ID: vg0828307900 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 28307900
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:


TACTTGAATAGTTCTTTTACTATGTTTTCTATTTTACCCTAGTTTTAGTCCATCTTTATCGGTTTGCGCCGTAAACCGTCCGCCGCCGCTGCGAGAGTGC[A/G]
ACACCTCTTTGTAGGTTTGTCCTAAAAACCTTCCGTTTTGCCCACGAGACGGGTAGTTATCCTCGTATCGATCTAAATCGGCCTAGAGGCTGATTTTGAT

Reverse complement sequence

ATCAAAATCAGCCTCTAGGCCGATTTAGATCGATACGAGGATAACTACCCGTCTCGTGGGCAAAACGGAAGGTTTTTAGGACAAACCTACAAAGAGGTGT[T/C]
GCACTCTCGCAGCGGCGGCGGACGGTTTACGGCGCAAACCGATAAAGATGGACTAAAACTAGGGTAAAATAGAAAACATAGTAAAAGAACTATTCAAGTA

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 91.40% 6.10% 2.56% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 73.80% 18.40% 7.80% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 54.20% 34.60% 11.21% 0.00% NA
Tropical Japonica  504 95.20% 1.40% 3.37% 0.00% NA
Japonica Intermediate  241 91.30% 2.50% 6.22% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 5.60% 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
vg0828307900 A -> G LOC_Os08g45080.1 upstream_gene_variant ; 2559.0bp to feature; MODIFIER silent_mutation Average:39.448; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0828307900 A -> G LOC_Os08g45090.1 downstream_gene_variant ; 3355.0bp to feature; MODIFIER silent_mutation Average:39.448; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0828307900 A -> G LOC_Os08g45080-LOC_Os08g45090 intergenic_region ; MODIFIER silent_mutation Average:39.448; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0828307900 NA 4.10E-06 mr1730_2 Jap_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
vg0828307900 NA 1.07E-06 mr1866_2 Jap_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
vg0828307900 NA 2.94E-06 mr1959_2 Jap_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