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Detailed information for vg0315011284:

Variant ID: vg0315011284 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 15011284
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


CGCTGGTGTGGAGGCTGCAGGAGATGGCGGTGGGGCAGGCTCGGGCGCTGGTGTCGGTGAACGACGACATCGTGAGGCTCCGGGACAGGCTGATGTGGCT[G/A]
CAGGCCTTCCTCCGGGAGGCCGACGCCAAGCGACGCGCCGTCTCCGACGAGGTCAACAAGGTGTGGCTGCTGCAGACGCGCGACGCCGTCTTCGACGCCG

Reverse complement sequence

CGGCGTCGAAGACGGCGTCGCGCGTCTGCAGCAGCCACACCTTGTTGACCTCGTCGGAGACGGCGCGTCGCTTGGCGTCGGCCTCCCGGAGGAAGGCCTG[C/T]
AGCCACATCAGCCTGTCCCGGAGCCTCACGATGTCGTCGTTCACCGACACCAGCGCCCGAGCCTGCCCCACCGCCATCTCCTGCAGCCTCCACACCAGCG

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 77.20% 22.60% 0.17% 0.00% NA
All Indica  2759 75.10% 24.80% 0.14% 0.00% NA
All Japonica  1512 91.50% 8.30% 0.13% 0.00% NA
Aus  269 15.20% 84.80% 0.00% 0.00% NA
Indica I  595 46.60% 52.90% 0.50% 0.00% NA
Indica II  465 58.30% 41.70% 0.00% 0.00% NA
Indica III  913 96.80% 3.20% 0.00% 0.00% NA
Indica Intermediate  786 81.30% 18.60% 0.13% 0.00% NA
Temperate Japonica  767 99.60% 0.30% 0.13% 0.00% NA
Tropical Japonica  504 77.60% 22.40% 0.00% 0.00% NA
Japonica Intermediate  241 95.00% 4.60% 0.41% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 70.00% 27.80% 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
vg0315011284 G -> A LOC_Os03g26250.1 synonymous_variant ; p.Leu41Leu; LOW synonymous_codon Average:70.461; most accessible tissue: Callus, score: 84.841 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0315011284 NA 2.47E-06 mr1082 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
vg0315011284 NA 1.13E-06 mr1083 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
vg0315011284 NA 9.25E-06 mr1088 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
vg0315011284 NA 1.03E-07 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
vg0315011284 NA 4.05E-08 mr1237 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
vg0315011284 NA 8.37E-07 mr1526 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
vg0315011284 NA 9.11E-06 mr1560 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
vg0315011284 NA 8.00E-06 mr1634 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
vg0315011284 NA 4.42E-08 mr1852 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