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Detailed information for vg0803961806:

Variant ID: vg0803961806 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 3961806
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.25, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTTCTACTCTATTCCAATTATCCAACTGCCCTATTCAAAGATCTCGAAGAAGGAATCAATACGAACCTTATAGATTAGTTTGAAAAATATATAGTTC[G/A]
CATCTATAAACTAAATATATACTAATAACACCCCTAGCATCTAGTAGAAATTAGTGCTGCGGTTAACTGAAATATTTTAAACAAATCATATTAGAAAAAC

Reverse complement sequence

GTTTTTCTAATATGATTTGTTTAAAATATTTCAGTTAACCGCAGCACTAATTTCTACTAGATGCTAGGGGTGTTATTAGTATATATTTAGTTTATAGATG[C/T]
GAACTATATATTTTTCAAACTAATCTATAAGGTTCGTATTGATTCCTTCTTCGAGATCTTTGAATAGGGCAGTTGGATAATTGGAATAGAGTAGAAAAAA

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 83.50% 16.30% 0.17% 0.00% NA
All Indica  2759 92.00% 8.00% 0.00% 0.00% NA
All Japonica  1512 64.60% 35.00% 0.46% 0.00% NA
Aus  269 96.70% 3.30% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 88.20% 11.80% 0.00% 0.00% NA
Indica III  913 87.60% 12.40% 0.00% 0.00% NA
Indica Intermediate  786 93.60% 6.40% 0.00% 0.00% NA
Temperate Japonica  767 39.60% 59.60% 0.78% 0.00% NA
Tropical Japonica  504 94.40% 5.60% 0.00% 0.00% NA
Japonica Intermediate  241 81.30% 18.30% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 87.80% 11.10% 1.11% 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
vg0803961806 G -> A LOC_Os08g07090.1 downstream_gene_variant ; 4672.0bp to feature; MODIFIER silent_mutation Average:30.451; most accessible tissue: Callus, score: 66.461 N N N N
vg0803961806 G -> A LOC_Os08g07080.1 intron_variant ; MODIFIER silent_mutation Average:30.451; most accessible tissue: Callus, score: 66.461 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0803961806 NA 1.50E-06 mr1002 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
vg0803961806 NA 4.22E-06 mr1182 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
vg0803961806 NA 2.54E-06 mr1650 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
vg0803961806 NA 3.40E-08 mr1002_2 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
vg0803961806 NA 4.90E-07 mr1180_2 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
vg0803961806 NA 1.94E-06 mr1895_2 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