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Detailed information for vg0321273503:

Variant ID: vg0321273503 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21273503
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.04, others allele: 0.00, population size: 154. )

Flanking Sequence (100 bp) in Reference Genome:


TATCTAATGTGGCGTCTATGTGAAACTTATACGATAAAACAACAACAACAAAAAAAAGTGGGTCAACGTACATGTAATCCATAGAGAAGAAATATAGTGT[G/A]
CATATGGCGGGACTATATATTTAAAGTGGTTTTAGAAGATGAGGGGCACTATCCAAACTCAACCGTTATATGCGGAAGAGTAAATTGCACTAGCGGTCCT

Reverse complement sequence

AGGACCGCTAGTGCAATTTACTCTTCCGCATATAACGGTTGAGTTTGGATAGTGCCCCTCATCTTCTAAAACCACTTTAAATATATAGTCCCGCCATATG[C/T]
ACACTATATTTCTTCTCTATGGATTACATGTACGTTGACCCACTTTTTTTTGTTGTTGTTGTTTTATCGTATAAGTTTCACATAGACGCCACATTAGATA

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 64.20% 35.60% 0.06% 0.17% NA
All Indica  2759 97.60% 2.20% 0.04% 0.14% NA
All Japonica  1512 1.70% 98.30% 0.00% 0.07% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 98.70% 1.20% 0.00% 0.17% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 98.10% 1.80% 0.00% 0.11% NA
Indica Intermediate  786 96.40% 3.20% 0.13% 0.25% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 4.40% 95.40% 0.00% 0.20% NA
Japonica Intermediate  241 0.40% 99.60% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 94.80% 0.00% 1.04% NA
Intermediate  90 47.80% 47.80% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0321273503 G -> A LOC_Os03g38330.1 downstream_gene_variant ; 1091.0bp to feature; MODIFIER silent_mutation Average:85.8; most accessible tissue: Callus, score: 95.763 N N N N
vg0321273503 G -> A LOC_Os03g38350.1 downstream_gene_variant ; 1896.0bp to feature; MODIFIER silent_mutation Average:85.8; most accessible tissue: Callus, score: 95.763 N N N N
vg0321273503 G -> A LOC_Os03g38330-LOC_Os03g38350 intergenic_region ; MODIFIER silent_mutation Average:85.8; most accessible tissue: Callus, score: 95.763 N N N N
vg0321273503 G -> DEL N N silent_mutation Average:85.8; most accessible tissue: Callus, score: 95.763 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321273503 NA 6.26E-14 mr1376 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
vg0321273503 NA 6.26E-14 mr1431 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
vg0321273503 NA 1.18E-35 mr1670 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
vg0321273503 NA 2.36E-11 mr1713 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
vg0321273503 1.55E-13 5.33E-95 mr1718 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
vg0321273503 5.23E-22 2.00E-170 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
vg0321273503 NA 3.65E-17 mr1842 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
vg0321273503 6.22E-06 3.59E-116 mr1987 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
vg0321273503 NA 2.01E-16 mr1342_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
vg0321273503 NA 1.30E-10 mr1537_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
vg0321273503 NA 2.14E-36 mr1541_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
vg0321273503 NA 2.81E-24 mr1588_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
vg0321273503 NA 1.88E-10 mr1595_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
vg0321273503 NA 1.03E-36 mr1689_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
vg0321273503 NA 1.13E-13 mr1713_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
vg0321273503 3.20E-19 1.66E-142 mr1718_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
vg0321273503 2.23E-34 1.47E-238 mr1750_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
vg0321273503 NA 1.69E-16 mr1842_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
vg0321273503 NA 1.59E-10 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
vg0321273503 NA 2.60E-22 mr1933_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
vg0321273503 2.91E-06 9.34E-157 mr1987_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