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Detailed information for vg0321044536:

Variant ID: vg0321044536 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21044536
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.10, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:


CTGATTTTACCAACCATGTTTTTAAATTGTCTAAAGCTTTGTATGGTTTGAAACAAGCTCCTAGGGCACGGTATGATAGGCTTAAGAACTTTTTGCTTGC[G/A]
AAAGGTTTTACAATGGGAAAGGTTGACAAAACGCTTTTTGTTCTTAAGCATGGTGATAATCAACTTTTCGTTCAGATTTATGTGGATGATATCATCTTTG

Reverse complement sequence

CAAAGATGATATCATCCACATAAATCTGAACGAAAAGTTGATTATCACCATGCTTAAGAACAAAAAGCGTTTTGTCAACCTTTCCCATTGTAAAACCTTT[C/T]
GCAAGCAAAAAGTTCTTAAGCCTATCATACCGTGCCCTAGGAGCTTGTTTCAAACCATACAAAGCTTTAGACAATTTAAAAACATGGTTGGTAAAATCAG

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 63.60% 36.30% 0.15% 0.00% NA
All Indica  2759 97.00% 2.80% 0.18% 0.00% NA
All Japonica  1512 3.20% 96.80% 0.07% 0.00% NA
Aus  269 88.10% 11.90% 0.00% 0.00% NA
Indica I  595 97.00% 2.70% 0.34% 0.00% NA
Indica II  465 96.80% 3.00% 0.22% 0.00% NA
Indica III  913 98.60% 1.40% 0.00% 0.00% NA
Indica Intermediate  786 95.30% 4.50% 0.25% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 8.90% 91.10% 0.00% 0.00% NA
Japonica Intermediate  241 0.40% 99.20% 0.41% 0.00% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 45.60% 53.30% 1.11% 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
vg0321044536 G -> A LOC_Os03g37890.1 synonymous_variant ; p.Ala289Ala; LOW synonymous_codon Average:18.063; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321044536 NA 2.38E-10 mr1188 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
vg0321044536 NA 4.67E-06 mr1215 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
vg0321044536 8.22E-07 NA mr1750 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
vg0321044536 2.03E-06 9.15E-17 mr1750 Ind_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
vg0321044536 1.97E-06 1.97E-06 mr1987 Ind_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
vg0321044536 NA 6.78E-09 mr1198_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
vg0321044536 NA 2.59E-10 mr1718_2 Ind_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
vg0321044536 2.21E-06 NA mr1750_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
vg0321044536 NA 9.17E-23 mr1750_2 Ind_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
vg0321044536 NA 4.54E-12 mr1893_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