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Detailed information for vg0904473538:

Variant ID: vg0904473538 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 4473538
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


ATTGTCAAATCATGGAGCAATTAGGCTTAAAAGATTCGTCTCGTAAATTGGTCGCAATTTGTGCAATTCGTTATTTTTTTAGCATATATTTAATACTTTA[T/G]
ATAGGTGTTCAAACGTTTATGTGAGAGGGTGTAAAATGTTTATGTGGGAACTAGAGAGGGCCTCAAAAGATCACTCCAACAGCGTGGATTTGACATCATT

Reverse complement sequence

AATGATGTCAAATCCACGCTGTTGGAGTGATCTTTTGAGGCCCTCTCTAGTTCCCACATAAACATTTTACACCCTCTCACATAAACGTTTGAACACCTAT[A/C]
TAAAGTATTAAATATATGCTAAAAAAATAACGAATTGCACAAATTGCGACCAATTTACGAGACGAATCTTTTAAGCCTAATTGCTCCATGATTTGACAAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.20% 17.80% 0.00% 0.00% NA
All Indica  2759 72.30% 27.70% 0.00% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 81.80% 18.20% 0.00% 0.00% NA
Indica I  595 68.90% 31.10% 0.00% 0.00% NA
Indica II  465 65.60% 34.40% 0.00% 0.00% NA
Indica III  913 85.80% 14.20% 0.00% 0.00% NA
Indica Intermediate  786 63.20% 36.80% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 78.90% 21.10% 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
vg0904473538 T -> G LOC_Os09g08580.1 upstream_gene_variant ; 1386.0bp to feature; MODIFIER silent_mutation Average:49.07; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0904473538 T -> G LOC_Os09g08590.1 upstream_gene_variant ; 4654.0bp to feature; MODIFIER silent_mutation Average:49.07; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0904473538 T -> G LOC_Os09g08570.1 downstream_gene_variant ; 4734.0bp to feature; MODIFIER silent_mutation Average:49.07; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0904473538 T -> G LOC_Os09g08570-LOC_Os09g08580 intergenic_region ; MODIFIER silent_mutation Average:49.07; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0904473538 4.99E-06 NA mr1208_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
vg0904473538 NA 7.00E-08 mr1208_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