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Detailed information for vg0628631429:

Variant ID: vg0628631429 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 28631429
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.06, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:


AGGATGTAGGGTTATTACCTGACAATTCAGGGGACCGAACCTGTATAAAAATCCCTGTCTCCATCTCTTTTACCCCAGTCTCGCGTATATCCTAGTACCA[A/G]
CGATCCCCATGCCATGCAAATACTGTAGTCGAGACATCAAACGTCGACAGTGGCGCGCCAGGTAGGGGAATTTTGGTGCTTCAGGATTTCGACGAGATGG

Reverse complement sequence

CCATCTCGTCGAAATCCTGAAGCACCAAAATTCCCCTACCTGGCGCGCCACTGTCGACGTTTGATGTCTCGACTACAGTATTTGCATGGCATGGGGATCG[T/C]
TGGTACTAGGATATACGCGAGACTGGGGTAAAAGAGATGGAGACAGGGATTTTTATACAGGTTCGGTCCCCTGAATTGTCAGGTAATAACCCTACATCCT

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 85.50% 14.40% 0.06% 0.00% NA
All Indica  2759 75.60% 24.20% 0.11% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 71.40% 28.20% 0.34% 0.00% NA
Indica II  465 88.80% 11.00% 0.22% 0.00% NA
Indica III  913 69.70% 30.30% 0.00% 0.00% NA
Indica Intermediate  786 78.00% 22.00% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0628631429 A -> G LOC_Os06g47220.1 upstream_gene_variant ; 1520.0bp to feature; MODIFIER silent_mutation Average:67.306; most accessible tissue: Minghui63 young leaf, score: 84.374 N N N N
vg0628631429 A -> G LOC_Os06g47210.1 downstream_gene_variant ; 3423.0bp to feature; MODIFIER silent_mutation Average:67.306; most accessible tissue: Minghui63 young leaf, score: 84.374 N N N N
vg0628631429 A -> G LOC_Os06g47220-LOC_Os06g47230 intergenic_region ; MODIFIER silent_mutation Average:67.306; most accessible tissue: Minghui63 young leaf, score: 84.374 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0628631429 NA 1.83E-07 mr1274 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
vg0628631429 NA 2.34E-06 mr1274 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
vg0628631429 NA 4.86E-06 mr1968_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
vg0628631429 NA 6.89E-06 mr1974_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