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Detailed information for vg1204578962:

Variant ID: vg1204578962 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 4578962
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: 122. )

Flanking Sequence (100 bp) in Reference Genome:


GGTTTTTAAATCTTAACGTAAAAATTTTCAAATTTGATATGAAGGTTTTCAAATCTGAGTCGAAAGGTTACAAATCTCGAGTCGAAAGGTTACAAATCTC[G/A]
AGTCGAAAGTTTACAAATCTCGAGTTGAAAATTTTCAAATCTGAATTAAAAGTTTTTAAAAATTTATCTAGCAAATTTAAATTACGAGTTGAAAATTTTG

Reverse complement sequence

CAAAATTTTCAACTCGTAATTTAAATTTGCTAGATAAATTTTTAAAAACTTTTAATTCAGATTTGAAAATTTTCAACTCGAGATTTGTAAACTTTCGACT[C/T]
GAGATTTGTAACCTTTCGACTCGAGATTTGTAACCTTTCGACTCAGATTTGAAAACCTTCATATCAAATTTGAAAATTTTTACGTTAAGATTTAAAAACC

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 93.20% 3.30% 3.47% 0.00% NA
All Indica  2759 95.10% 2.90% 2.07% 0.00% NA
All Japonica  1512 88.40% 4.80% 6.88% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 96.80% 1.80% 1.34% 0.00% NA
Indica II  465 95.10% 2.40% 2.58% 0.00% NA
Indica III  913 93.80% 3.80% 2.41% 0.00% NA
Indica Intermediate  786 95.30% 2.80% 1.91% 0.00% NA
Temperate Japonica  767 79.00% 9.00% 11.99% 0.00% NA
Tropical Japonica  504 98.80% 0.00% 1.19% 0.00% NA
Japonica Intermediate  241 96.30% 1.20% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 6.70% 2.22% 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
vg1204578962 G -> A LOC_Os12g08860.1 upstream_gene_variant ; 2251.0bp to feature; MODIFIER silent_mutation Average:19.418; most accessible tissue: Callus, score: 44.842 N N N N
vg1204578962 G -> A LOC_Os12g08860-LOC_Os12g08870 intergenic_region ; MODIFIER silent_mutation Average:19.418; most accessible tissue: Callus, score: 44.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1204578962 NA 8.89E-06 Yield Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1204578962 4.77E-06 NA mr1169 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
vg1204578962 NA 2.44E-06 mr1171 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
vg1204578962 NA 3.74E-07 mr1712 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