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Detailed information for vg0402393946:

Variant ID: vg0402393946 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2393946
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


AACTAGGGGCAATAGTAGTACCATATTTCCTCTGCTCCCCGGGCATTAGAGCTCCTACACTAAGAATTCCAGTAAGCTTAACTTCTGCTTCTATCTTACC[A/G]
TCCTGCATCCAGGAAAAAAAAAATGATCCGCATAAAAGAGGCAATCACTTCACAATTTAAGGAGCCTCCACCCCCCAAACAGAATCAACACCACCCAAAT

Reverse complement sequence

ATTTGGGTGGTGTTGATTCTGTTTGGGGGGTGGAGGCTCCTTAAATTGTGAAGTGATTGCCTCTTTTATGCGGATCATTTTTTTTTTCCTGGATGCAGGA[T/C]
GGTAAGATAGAAGCAGAAGTTAAGCTTACTGGAATTCTTAGTGTAGGAGCTCTAATGCCCGGGGAGCAGAGGAAATATGGTACTACTATTGCCCCTAGTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.90% 5.40% 0.68% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 83.50% 14.40% 2.12% 0.00% NA
Aus  269 91.80% 8.20% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 97.70% 2.00% 0.39% 0.00% NA
Tropical Japonica  504 68.70% 29.80% 1.59% 0.00% NA
Japonica Intermediate  241 69.70% 21.60% 8.71% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0402393946 A -> G LOC_Os04g04950.1 splice_region_variant&synonymous_variant ; p.Asp539Asp; LOW synonymous_codon Average:44.205; most accessible tissue: Minghui63 young leaf, score: 58.21 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402393946 NA 6.22E-15 mr1410 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
vg0402393946 NA 1.36E-16 mr1410_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
vg0402393946 NA 1.82E-11 mr1410_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
vg0402393946 NA 8.51E-08 mr1696_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
vg0402393946 9.46E-12 NA mr1798_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
vg0402393946 1.88E-12 NA mr1798_2 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