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Detailed information for vg0420863715:

Variant ID: vg0420863715 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20863715
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


TACTGTTGGCACACTCTTTCGGTATAGTTCATTTTGATTTCCTTCTAGCTGCACATTCATGTTATTCAAACCTCCTCTCTCAGCTTGTTTGAAATTGAAT[G/A]
CCATGCTTTTCATTTTCTCTGTTGTTGCATTTGTTCATGTATCATTTCATATCTGCATTCTCCATATTAGATGTTAAATGCACCAAATACAAACATCTGT

Reverse complement sequence

ACAGATGTTTGTATTTGGTGCATTTAACATCTAATATGGAGAATGCAGATATGAAATGATACATGAACAAATGCAACAACAGAGAAAATGAAAAGCATGG[C/T]
ATTCAATTTCAAACAAGCTGAGAGAGGAGGTTTGAATAACATGAATGTGCAGCTAGAAGGAAATCAAAATGAACTATACCGAAAGAGTGTGCCAACAGTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.90% 5.60% 2.48% 0.00% NA
All Indica  2759 86.30% 9.60% 4.17% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 82.70% 5.00% 12.27% 0.00% NA
Indica II  465 97.20% 0.60% 2.15% 0.00% NA
Indica III  913 79.50% 19.60% 0.88% 0.00% NA
Indica Intermediate  786 90.30% 6.60% 3.05% 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 97.80% 0.00% 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
vg0420863715 G -> A LOC_Os04g34450.1 intron_variant ; MODIFIER silent_mutation Average:58.735; most accessible tissue: Minghui63 flag leaf, score: 72.472 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0420863715 4.65E-07 NA mr1486 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
vg0420863715 3.52E-06 NA mr1486_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
vg0420863715 2.61E-06 NA mr1588_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