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Detailed information for vg0216482818:

Variant ID: vg0216482818 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 16482818
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


ATCCTCATGAGAACTAACGAATAAATGACGAATCACGCCCAACTCAGGTGCACTGAGTGAATCTGTAGAGTTGGTCAATTCGGAGTCCACCGTAGTAGTT[G/A]
ATATCTCTGCACGATAAGCAAGTCAGTCTGACAGTGTTCAGTTCTATTACCTCGCAAACAAAATGGTAAAATAGTAATTCATTTTAGGATGATTTGTTAC

Reverse complement sequence

GTAACAAATCATCCTAAAATGAATTACTATTTTACCATTTTGTTTGCGAGGTAATAGAACTGAACACTGTCAGACTGACTTGCTTATCGTGCAGAGATAT[C/T]
AACTACTACGGTGGACTCCGAATTGACCAACTCTACAGATTCACTCAGTGCACCTGAGTTGGGCGTGATTCGTCATTTATTCGTTAGTTCTCATGAGGAT

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 83.10% 16.70% 0.25% 0.00% NA
All Indica  2759 97.10% 2.90% 0.04% 0.00% NA
All Japonica  1512 53.30% 46.00% 0.66% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 91.20% 8.60% 0.22% 0.00% NA
Indica III  913 97.50% 2.50% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 22.60% 76.30% 1.17% 0.00% NA
Tropical Japonica  504 89.30% 10.70% 0.00% 0.00% NA
Japonica Intermediate  241 75.90% 23.70% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 85.60% 13.30% 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
vg0216482818 G -> A LOC_Os02g27840.1 downstream_gene_variant ; 2543.0bp to feature; MODIFIER silent_mutation Average:40.629; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0216482818 G -> A LOC_Os02g27830.1 intron_variant ; MODIFIER silent_mutation Average:40.629; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0216482818 7.44E-06 NA mr1088 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
vg0216482818 5.12E-06 NA mr1235 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
vg0216482818 7.56E-07 7.54E-07 mr1703 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
vg0216482818 NA 4.12E-08 mr1399_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