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Detailed information for vg0825074071:

Variant ID: vg0825074071 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25074071
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


CTTGCCTGTCCAGATGGACTAGCATCCGCGCCACTTGGAACTTCTGCATTCTTCGGGCATTTCTTGTAAGTATGGCCACGCAGATCACACTTGCTGCAGC[G/A]
TAAAGTCCTCCCACCTGCTTCTGATTTATCCATATCATTTCTGATGCGTCTAGTTTGGCGTCGACCCTTTTTCACCCTTAACTTAGATGGATCTAGAATA

Reverse complement sequence

TATTCTAGATCCATCTAAGTTAAGGGTGAAAAAGGGTCGACGCCAAACTAGACGCATCAGAAATGATATGGATAAATCAGAAGCAGGTGGGAGGACTTTA[C/T]
GCTGCAGCAAGTGTGATCTGCGTGGCCATACTTACAAGAAATGCCCGAAGAATGCAGAAGTTCCAAGTGGCGCGGATGCTAGTCCATCTGGACAGGCAAG

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 82.30% 17.60% 0.15% 0.00% NA
All Indica  2759 70.20% 29.60% 0.25% 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 67.60% 31.80% 0.67% 0.00% NA
Indica II  465 78.70% 21.10% 0.22% 0.00% NA
Indica III  913 59.00% 41.00% 0.00% 0.00% NA
Indica Intermediate  786 80.00% 19.70% 0.25% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 90.00% 10.00% 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
vg0825074071 G -> A LOC_Os08g39620.1 missense_variant ; p.Arg817Cys; MODERATE nonsynonymous_codon ; R817C Average:21.242; most accessible tissue: Minghui63 flag leaf, score: 38.136 unknown unknown DELETERIOUS 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825074071 1.24E-06 NA mr1874 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
vg0825074071 1.58E-06 1.27E-11 mr1874 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
vg0825074071 2.31E-07 NA mr1874_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
vg0825074071 4.67E-07 5.27E-13 mr1874_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