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Detailed information for vg0921230909:

Variant ID: vg0921230909 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 21230909
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


GTGAGAATGATTGAAGAAGGTGTGTGATTGGTTGAAAAGAGAAAGTAGGTGAAAAAGAATGGTTGTGATTGGTTGAGAGAAGAAGGTAGGTAGAAAAATA[G/A]
CTTCATTTTGAGACAAAGTACTGTGCTAGAAATAGCTACATTTTGGGACGGATGTAGTAGTTACATAAATTTGTTGAATAAGACGAATGGTCAAAAGTTG

Reverse complement sequence

CAACTTTTGACCATTCGTCTTATTCAACAAATTTATGTAACTACTACATCCGTCCCAAAATGTAGCTATTTCTAGCACAGTACTTTGTCTCAAAATGAAG[C/T]
TATTTTTCTACCTACCTTCTTCTCTCAACCAATCACAACCATTCTTTTTCACCTACTTTCTCTTTTCAACCAATCACACACCTTCTTCAATCATTCTCAC

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 96.10% 3.90% 0.00% 0.00% NA
All Indica  2759 93.40% 6.60% 0.00% 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  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 89.90% 10.10% 0.00% 0.00% NA
Indica III  913 92.30% 7.70% 0.00% 0.00% NA
Indica Intermediate  786 91.70% 8.30% 0.00% 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% 2.20% 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
vg0921230909 G -> A LOC_Os09g36800.1 upstream_gene_variant ; 1518.0bp to feature; MODIFIER silent_mutation Average:45.569; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg0921230909 G -> A LOC_Os09g36810.1 intron_variant ; MODIFIER silent_mutation Average:45.569; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0921230909 2.90E-06 2.90E-06 mr1848_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