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Detailed information for vg0811251683:

Variant ID: vg0811251683 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 11251683
Reference Allele: GAlternative Allele: A
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: 263. )

Flanking Sequence (100 bp) in Reference Genome:


AATATCATACCCGCTAGATAAATATGTCAGACAAACTTCATCAACAATAGCCTTTTTACAACAAAAGGTCATAGGTTCTTCTCCGTTTGACCTCTTTTGC[G/A]
GCATTTCTTCTTTCAGCATATGATTTTCTTATGCTAAAGCCTTTATCCCAAGCGTACTTGTTGTAGAAGTGAATTCCTTCATCCTCACTATTGAATGTCT

Reverse complement sequence

AGACATTCAATAGTGAGGATGAAGGAATTCACTTCTACAACAAGTACGCTTGGGATAAAGGCTTTAGCATAAGAAAATCATATGCTGAAAGAAGAAATGC[C/T]
GCAAAAGAGGTCAAACGGAGAAGAACCTATGACCTTTTGTTGTAAAAAGGCTATTGTTGATGAAGTTTGTCTGACATATTTATCTAGCGGGTATGATATT

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 98.90% 0.10% 0.99% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.40% 0.50% 3.11% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 93.40% 0.90% 5.74% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.00% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0811251683 G -> A LOC_Os08g18850.1 synonymous_variant ; p.Ala53Ala; LOW synonymous_codon Average:14.368; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0811251683 NA 6.10E-07 mr1028 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
vg0811251683 4.76E-06 4.76E-06 mr1369 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
vg0811251683 NA 3.17E-06 mr1453 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
vg0811251683 NA 6.12E-07 mr1648 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
vg0811251683 NA 3.31E-06 mr1652 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
vg0811251683 NA 5.49E-08 mr1697 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