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Detailed information for vg1108581599:

Variant ID: vg1108581599 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 8581599
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, A: 0.28, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTTAAATGTATAGAATCCATAAAATTGGTTTCTTTTGCTATTTCAGTAGCCTTATTGCTTGTAATTCTTGTGTGCTTTGTTTGCGTTTAGATTCCGTC[G/A]
GTTCCGGTGATCCAGTTTATTTCGAAGTCGTTGCCGAGGTTCAGCTCAAGAGCAAGGCAAGTCATACATACATCATTGATCATATTGAGCCTATTTTATA

Reverse complement sequence

TATAAAATAGGCTCAATATGATCAATGATGTATGTATGACTTGCCTTGCTCTTGAGCTGAACCTCGGCAACGACTTCGAAATAAACTGGATCACCGGAAC[C/T]
GACGGAATCTAAACGCAAACAAAGCACACAAGAATTACAAGCAATAAGGCTACTGAAATAGCAAAAGAAACCAATTTTATGGATTCTATACATTTAACGG

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 59.00% 41.00% 0.02% 0.00% NA
All Indica  2759 35.80% 64.20% 0.04% 0.00% NA
All Japonica  1512 96.60% 3.40% 0.00% 0.00% NA
Aus  269 73.20% 26.80% 0.00% 0.00% NA
Indica I  595 16.50% 83.50% 0.00% 0.00% NA
Indica II  465 58.50% 41.50% 0.00% 0.00% NA
Indica III  913 31.80% 68.20% 0.00% 0.00% NA
Indica Intermediate  786 41.60% 58.30% 0.13% 0.00% NA
Temperate Japonica  767 97.90% 2.10% 0.00% 0.00% NA
Tropical Japonica  504 94.40% 5.60% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 60.00% 40.00% 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
vg1108581599 G -> A LOC_Os11g15210.1 downstream_gene_variant ; 2292.0bp to feature; MODIFIER silent_mutation Average:26.515; most accessible tissue: Zhenshan97 young leaf, score: 35.853 N N N N
vg1108581599 G -> A LOC_Os11g15200-LOC_Os11g15210 intergenic_region ; MODIFIER silent_mutation Average:26.515; most accessible tissue: Zhenshan97 young leaf, score: 35.853 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1108581599 NA 1.57E-06 mr1911 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
vg1108581599 5.79E-08 5.79E-08 mr1918 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
vg1108581599 NA 4.83E-13 mr1904_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
vg1108581599 NA 4.22E-07 mr1911_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