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Detailed information for vg0320452783:

Variant ID: vg0320452783 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 20452783
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:


TCATCAATAATCCCAAACACAGGAGTAGGGTGTTACGCTCTATAGCGGCCCAAACCTGTATAATCCCACTACGTGCAAGCTTGCCGGTAATCTTAGGGAC[G/A]
AGCGAGTGATTTCCGAGAGGCGGGCCTCCGCCCCCGGCCGAACTCACGAAAGGGGGGGTCTCACGACCTCCCGCTATCGGGGGGCCATCCCTCGACAGCT

Reverse complement sequence

AGCTGTCGAGGGATGGCCCCCCGATAGCGGGAGGTCGTGAGACCCCCCCTTTCGTGAGTTCGGCCGGGGGCGGAGGCCCGCCTCTCGGAAATCACTCGCT[C/T]
GTCCCTAAGATTACCGGCAAGCTTGCACGTAGTGGGATTATACAGGTTTGGGCCGCTATAGAGCGTAACACCCTACTCCTGTGTTTGGGATTATTGATGA

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 84.90% 15.10% 0.00% 0.00% NA
All Indica  2759 80.60% 19.40% 0.00% 0.00% NA
All Japonica  1512 88.90% 11.10% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 94.30% 5.70% 0.00% 0.00% NA
Indica II  465 76.80% 23.20% 0.00% 0.00% NA
Indica III  913 70.10% 29.90% 0.00% 0.00% NA
Indica Intermediate  786 84.60% 15.40% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 69.60% 30.40% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 6.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0320452783 G -> A LOC_Os03g36860.1 upstream_gene_variant ; 287.0bp to feature; MODIFIER silent_mutation Average:67.367; most accessible tissue: Minghui63 flag leaf, score: 79.962 N N N N
vg0320452783 G -> A LOC_Os03g36830-LOC_Os03g36860 intergenic_region ; MODIFIER silent_mutation Average:67.367; most accessible tissue: Minghui63 flag leaf, score: 79.962 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0320452783 NA 2.55E-08 mr1217 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
vg0320452783 NA 1.65E-06 mr1218 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
vg0320452783 2.56E-07 2.57E-07 mr1362 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
vg0320452783 3.93E-06 NA mr1439 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
vg0320452783 NA 2.96E-06 mr1583 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
vg0320452783 NA 1.42E-07 mr1696 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
vg0320452783 NA 6.95E-07 mr1830 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
vg0320452783 NA 6.27E-08 mr1845 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
vg0320452783 NA 1.10E-06 mr1852 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
vg0320452783 NA 2.56E-10 mr1852 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
vg0320452783 NA 6.38E-06 mr1439_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