Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0810398690:

Variant ID: vg0810398690 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 10398690
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.20, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


CTCATCCGGAATTGGATGTGCAGCGAGGAAGTTTGCTAAGGCTTGTCCTTTTATTGATTTTTGTGGGACAAATATAATGTCAAACTGCGACAAAAACATC[G/A]
CCCATATAGCTAATCTTCCTGAGAGGACCATTTTACTCAATATATATCAGAATGGGTCCGCCCCCGACACGAGGTGTATGGTGTGTTCTAGCATATAGTG

Reverse complement sequence

CACTATATGCTAGAACACACCATACACCTCGTGTCGGGGGCGGACCCATTCTGATATATATTGAGTAAAATGGTCCTCTCAGGAAGATTAGCTATATGGG[C/T]
GATGTTTTTGTCGCAGTTTGACATTATATTTGTCCCACAAAAATCAATAAAAGGACAAGCCTTAGCAAACTTCCTCGCTGCACATCCAATTCCGGATGAG

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 75.60% 24.40% 0.06% 0.00% NA
All Indica  2759 94.30% 5.60% 0.11% 0.00% NA
All Japonica  1512 36.40% 63.60% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 96.50% 3.50% 0.00% 0.00% NA
Indica II  465 95.70% 3.90% 0.43% 0.00% NA
Indica III  913 90.30% 9.60% 0.11% 0.00% NA
Indica Intermediate  786 96.40% 3.60% 0.00% 0.00% NA
Temperate Japonica  767 6.90% 93.10% 0.00% 0.00% NA
Tropical Japonica  504 68.30% 31.70% 0.00% 0.00% NA
Japonica Intermediate  241 63.50% 36.50% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 68.90% 31.10% 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
vg0810398690 G -> A LOC_Os08g16970.1 upstream_gene_variant ; 2659.0bp to feature; MODIFIER silent_mutation Average:54.594; most accessible tissue: Zhenshan97 flag leaf, score: 74.162 N N N N
vg0810398690 G -> A LOC_Os08g16990.1 upstream_gene_variant ; 4540.0bp to feature; MODIFIER silent_mutation Average:54.594; most accessible tissue: Zhenshan97 flag leaf, score: 74.162 N N N N
vg0810398690 G -> A LOC_Os08g16980.1 downstream_gene_variant ; 47.0bp to feature; MODIFIER silent_mutation Average:54.594; most accessible tissue: Zhenshan97 flag leaf, score: 74.162 N N N N
vg0810398690 G -> A LOC_Os08g16970-LOC_Os08g16980 intergenic_region ; MODIFIER silent_mutation Average:54.594; most accessible tissue: Zhenshan97 flag leaf, score: 74.162 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0810398690 NA 7.04E-06 mr1153_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
vg0810398690 3.75E-08 1.99E-09 mr1172_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