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Detailed information for vg0820433691:

Variant ID: vg0820433691 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 20433691
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, G: 0.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GATCCCTAGCTAGACCGTCAGTATTCGTCATATATAGTATTTGTAAGCAAACAAATTTAACGTAATATCCCAATGCAGTATTAATATGGAGCCACTCTAT[C/G]
AATCAGGATTTTGAGCACAAGTGTCAGCCATTTTGTATCCTAATTTTAATTCGATGAAAAGAACTTCTAAAGAAATTTAACTATGAAGCGTGCATGTGAA

Reverse complement sequence

TTCACATGCACGCTTCATAGTTAAATTTCTTTAGAAGTTCTTTTCATCGAATTAAAATTAGGATACAAAATGGCTGACACTTGTGCTCAAAATCCTGATT[G/C]
ATAGAGTGGCTCCATATTAATACTGCATTGGGATATTACGTTAAATTTGTTTGCTTACAAATACTATATATGACGAATACTGACGGTCTAGCTAGGGATC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.20% 9.80% 0.00% 0.00% NA
All Indica  2759 83.40% 16.60% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 65.80% 34.20% 0.00% 0.00% NA
Indica Intermediate  786 84.40% 15.60% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0820433691 C -> G LOC_Os08g32940.1 upstream_gene_variant ; 2654.0bp to feature; MODIFIER silent_mutation Average:43.855; most accessible tissue: Callus, score: 86.533 N N N N
vg0820433691 C -> G LOC_Os08g32940-LOC_Os08g32950 intergenic_region ; MODIFIER silent_mutation Average:43.855; most accessible tissue: Callus, score: 86.533 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0820433691 NA 4.41E-08 mr1561 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
vg0820433691 NA 5.23E-07 mr1561 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
vg0820433691 1.07E-06 1.07E-06 mr1872 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
vg0820433691 NA 9.02E-06 mr1932 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
vg0820433691 NA 7.84E-07 mr1561_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