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Detailed information for vg0827168299:

Variant ID: vg0827168299 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 27168299
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: 281. )

Flanking Sequence (100 bp) in Reference Genome:


TATGCATGTTATTTTATTTATTTGTAAAATAGAAGATTCTTAAATCGTTAAACATTTGTTTTCATTAATTGTCATTAGAAACAAGCCATGGGTCAAGGAA[G/A]
AAGAGGTGGAGATGAGGTGGATGCTGCAGACGAAGATGACCCTGAAACAACTGACCATCCACAAGACTACGAAACAGAGGATGCTTCCCAGATTTCAGAA

Reverse complement sequence

TTCTGAAATCTGGGAAGCATCCTCTGTTTCGTAGTCTTGTGGATGGTCAGTTGTTTCAGGGTCATCTTCGTCTGCAGCATCCACCTCATCTCCACCTCTT[C/T]
TTCCTTGACCCATGGCTTGTTTCTAATGACAATTAATGAAAACAAATGTTTAACGATTTAAGAATCTTCTATTTTACAAATAAATAAAATAACATGCATA

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 91.00% 9.00% 0.02% 0.00% NA
All Indica  2759 85.20% 14.80% 0.04% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 68.60% 31.40% 0.00% 0.00% NA
Indica III  913 83.60% 16.30% 0.11% 0.00% NA
Indica Intermediate  786 86.30% 13.70% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0827168299 G -> A LOC_Os08g42980.1 missense_variant ; p.Arg304Lys; MODERATE nonsynonymous_codon ; R304K Average:56.8; most accessible tissue: Callus, score: 75.635 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0827168299 NA 2.87E-08 mr1498 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
vg0827168299 NA 2.03E-09 mr1769 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
vg0827168299 NA 7.44E-06 mr1887 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
vg0827168299 NA 1.00E-07 mr1887 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
vg0827168299 NA 1.84E-06 mr1925 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
vg0827168299 NA 1.13E-09 mr1951 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
vg0827168299 NA 1.41E-07 mr1951 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
vg0827168299 NA 1.34E-07 mr1498_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