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Detailed information for vg0226676076:

Variant ID: vg0226676076 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 26676076
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


CAAATATATAAGTTATTCTTAAAATACATTTAATAACAAATTAAATCACAATAAAATAAATAATACTTAACAAATTTCACGTAAAAAATATTTAAAGATG[G/A]
AGGTGGTACTATCCTGCGGGACATGAGGGACGTCAAATTTTCAATTCATATCTCCATGGTGGAGAAGCTCGCTGAGGTTCGTTACCAATCCAGTTCGATG

Reverse complement sequence

CATCGAACTGGATTGGTAACGAACCTCAGCGAGCTTCTCCACCATGGAGATATGAATTGAAAATTTGACGTCCCTCATGTCCCGCAGGATAGTACCACCT[C/T]
CATCTTTAAATATTTTTTACGTGAAATTTGTTAAGTATTATTTATTTTATTGTGATTTAATTTGTTATTAAATGTATTTTAAGAATAACTTATATATTTG

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 92.10% 7.80% 0.04% 0.00% NA
All Indica  2759 92.50% 7.40% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 43.10% 56.90% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 92.90% 7.10% 0.00% 0.00% NA
Indica III  913 90.10% 9.60% 0.22% 0.00% NA
Indica Intermediate  786 90.10% 9.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0226676076 G -> A LOC_Os02g44120.1 downstream_gene_variant ; 4932.0bp to feature; MODIFIER silent_mutation Average:48.907; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N
vg0226676076 G -> A LOC_Os02g44120-LOC_Os02g44124 intergenic_region ; MODIFIER silent_mutation Average:48.907; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0226676076 1.71E-06 NA mr1565 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