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Detailed information for vg0526332116:

Variant ID: vg0526332116 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 26332116
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


GCACATGTGGGTTACTGTAGCACTTATGGCTAATTATGGACTAATTAGTCTCAAAAGATTCGTCTCGCGATTTACATGCAAACAGTGCAAACGGTTTAAT[G/C]
CTCCATACATGCGTCCAAAGATTCGATGTGATATTTTTTAAAAAGTTTTTGGGGAACTAAACAGGGTCTACGTTGTAAGGCTGATGTAAATGATTTCTTT

Reverse complement sequence

AAAGAAATCATTTACATCAGCCTTACAACGTAGACCCTGTTTAGTTCCCCAAAAACTTTTTAAAAAATATCACATCGAATCTTTGGACGCATGTATGGAG[C/G]
ATTAAACCGTTTGCACTGTTTGCATGTAAATCGCGAGACGAATCTTTTGAGACTAATTAGTCCATAATTAGCCATAAGTGCTACAGTAACCCACATGTGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.70% 13.00% 2.31% 0.00% NA
All Indica  2759 74.80% 21.30% 3.88% 0.00% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 70.30% 19.20% 10.59% 0.00% NA
Indica II  465 65.40% 32.50% 2.15% 0.00% NA
Indica III  913 82.70% 17.00% 0.33% 0.00% NA
Indica Intermediate  786 74.70% 21.40% 3.94% 0.00% NA
Temperate Japonica  767 98.80% 1.20% 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 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 81.10% 16.70% 2.22% 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
vg0526332116 G -> C LOC_Os05g45390.1 upstream_gene_variant ; 778.0bp to feature; MODIFIER silent_mutation Average:47.608; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg0526332116 G -> C LOC_Os05g45380.1 downstream_gene_variant ; 3192.0bp to feature; MODIFIER silent_mutation Average:47.608; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg0526332116 G -> C LOC_Os05g45400.1 downstream_gene_variant ; 1677.0bp to feature; MODIFIER silent_mutation Average:47.608; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg0526332116 G -> C LOC_Os05g45390-LOC_Os05g45400 intergenic_region ; MODIFIER silent_mutation Average:47.608; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0526332116 5.31E-07 7.33E-07 mr1484 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