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Detailed information for vg0800828687:

Variant ID: vg0800828687 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 828687
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TCTAGTAGTTGGTTAATTAATTTTAATCTGATTATATTATGTGTGTGTTTCCATGGCTTTTAGGAGCAAATCCTACGAGTGGTAGGTTAATTTCTTTGTG[C/A]
CCCCACTGTGGGGTGCACCACGGATTTGTGTTGGTTGGGTGCTCCGACGATCCGCCGACGTGATCGCCTATCTGCCACACGTGTTGCTCCATATTGCACA

Reverse complement sequence

TGTGCAATATGGAGCAACACGTGTGGCAGATAGGCGATCACGTCGGCGGATCGTCGGAGCACCCAACCAACACAAATCCGTGGTGCACCCCACAGTGGGG[G/T]
CACAAAGAAATTAACCTACCACTCGTAGGATTTGCTCCTAAAAGCCATGGAAACACACACATAATATAATCAGATTAAAATTAATTAACCAACTACTAGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.50% 1.20% 0.30% 0.00% NA
All Indica  2759 97.50% 2.00% 0.51% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 91.40% 6.70% 1.85% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.00% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 98.90% 1.10% 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
vg0800828687 C -> A LOC_Os08g02290.1 upstream_gene_variant ; 1955.0bp to feature; MODIFIER silent_mutation Average:64.622; most accessible tissue: Callus, score: 84.04 N N N N
vg0800828687 C -> A LOC_Os08g02290-LOC_Os08g02300 intergenic_region ; MODIFIER silent_mutation Average:64.622; most accessible tissue: Callus, score: 84.04 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0800828687 NA 6.81E-07 mr1180 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
vg0800828687 NA 2.75E-06 mr1211 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
vg0800828687 NA 4.24E-06 mr1128_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
vg0800828687 NA 6.72E-07 mr1180_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
vg0800828687 NA 4.16E-06 mr1754_2 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