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Detailed information for vg0323940115:

Variant ID: vg0323940115 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 23940115
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


ATCTAGTATTTGCACCTCACGTCACTTGGTGTTAAGAACGGCTAGGTGCCAGTGTGTTTGTTTAATATTAATTGGGAGGAAAATCTGCAGATGTTCAACA[G/A]
CAAGATAGGGTCGTAAATTGTATTAGCCATTACATAGATAACTTAAATAAGTATTACCATGTCAAATGCTAGATAGTCGCGTGCCATATCTCTTATCCAT

Reverse complement sequence

ATGGATAAGAGATATGGCACGCGACTATCTAGCATTTGACATGGTAATACTTATTTAAGTTATCTATGTAATGGCTAATACAATTTACGACCCTATCTTG[C/T]
TGTTGAACATCTGCAGATTTTCCTCCCAATTAATATTAAACAAACACACTGGCACCTAGCCGTTCTTAACACCAAGTGACGTGAGGTGCAAATACTAGAT

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 93.80% 6.10% 0.04% 0.00% NA
All Indica  2759 98.10% 1.80% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 14.10% 85.50% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 97.40% 2.60% 0.00% 0.00% NA
Indica Intermediate  786 96.90% 3.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0323940115 G -> A LOC_Os03g42920.1 upstream_gene_variant ; 1290.0bp to feature; MODIFIER silent_mutation Average:58.205; most accessible tissue: Zhenshan97 young leaf, score: 67.334 N N N N
vg0323940115 G -> A LOC_Os03g42910.1 downstream_gene_variant ; 2116.0bp to feature; MODIFIER silent_mutation Average:58.205; most accessible tissue: Zhenshan97 young leaf, score: 67.334 N N N N
vg0323940115 G -> A LOC_Os03g42930.1 intron_variant ; MODIFIER silent_mutation Average:58.205; most accessible tissue: Zhenshan97 young leaf, score: 67.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0323940115 NA 5.56E-10 mr1388_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
vg0323940115 NA 2.80E-08 mr1707_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
vg0323940115 NA 6.05E-09 mr1741_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
vg0323940115 NA 1.26E-09 mr1860_2 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