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Detailed information for vg0817611509:

Variant ID: vg0817611509 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 17611509
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

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

Flanking Sequence (100 bp) in Reference Genome:


AAACTTAATAATATCCCCCGTCACACATCGGAGCCAGCAATCTCCCCCACCACATCAACCTATGTGACTTGAAGACTTGTTTACTGAATTTCCCCACCAT[G/A]
TGACCCATAGAAATTCTTCTGGGTTAATTCTAAATCTAGGCTCTGATATCACTTGTTATAAAAGTTGGTAGATATAGCAGATAAATAACTAACCTTCCCA

Reverse complement sequence

TGGGAAGGTTAGTTATTTATCTGCTATATCTACCAACTTTTATAACAAGTGATATCAGAGCCTAGATTTAGAATTAACCCAGAAGAATTTCTATGGGTCA[C/T]
ATGGTGGGGAAATTCAGTAAACAAGTCTTCAAGTCACATAGGTTGATGTGGTGGGGGAGATTGCTGGCTCCGATGTGTGACGGGGGATATTATTAAGTTT

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 89.50% 10.50% 0.00% 0.00% NA
All Indica  2759 96.80% 3.20% 0.00% 0.00% NA
All Japonica  1512 87.20% 12.80% 0.00% 0.00% NA
Aus  269 29.00% 71.00% 0.00% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 97.00% 3.00% 0.00% 0.00% NA
Indica Intermediate  786 94.90% 5.10% 0.00% 0.00% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 68.70% 31.30% 0.00% 0.00% NA
Japonica Intermediate  241 90.00% 10.00% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0817611509 G -> A LOC_Os08g28784.1 upstream_gene_variant ; 4684.0bp to feature; MODIFIER silent_mutation Average:59.513; most accessible tissue: Zhenshan97 young leaf, score: 69.723 N N N N
vg0817611509 G -> A LOC_Os08g28790.1 upstream_gene_variant ; 2062.0bp to feature; MODIFIER silent_mutation Average:59.513; most accessible tissue: Zhenshan97 young leaf, score: 69.723 N N N N
vg0817611509 G -> A LOC_Os08g28784-LOC_Os08g28790 intergenic_region ; MODIFIER silent_mutation Average:59.513; most accessible tissue: Zhenshan97 young leaf, score: 69.723 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0817611509 1.08E-08 1.29E-09 mr1040 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
vg0817611509 4.60E-11 7.10E-16 mr1836 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
vg0817611509 NA 4.87E-07 mr1852 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
vg0817611509 3.98E-07 NA mr1040_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
vg0817611509 4.42E-08 NA mr1362_2 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
vg0817611509 NA 8.11E-06 mr1786_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
vg0817611509 1.18E-12 NA mr1836_2 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
vg0817611509 NA 8.43E-06 mr1836_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