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Detailed information for vg0225615391:

Variant ID: vg0225615391 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25615391
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


TATATATCTATCTAGATTCATTAATATCAATATAAATGTGACAAATGTTAAAATGACTTACATTGTGAAACATAGAAAGTAAGTATTATCAACCCGGAGG[G/A]
AGTATCAACAAGCCGAAGAAAATGGAGGGGAGTAAGGGAATATCGAAAGTAGAAGTGATTAGTAAAAAAAAAATGCAGTTGGGTACTCTGGGACAGCTAG

Reverse complement sequence

CTAGCTGTCCCAGAGTACCCAACTGCATTTTTTTTTTACTAATCACTTCTACTTTCGATATTCCCTTACTCCCCTCCATTTTCTTCGGCTTGTTGATACT[C/T]
CCTCCGGGTTGATAATACTTACTTTCTATGTTTCACAATGTAAGTCATTTTAACATTTGTCACATTTATATTGATATTAATGAATCTAGATAGATATATA

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 88.80% 10.90% 0.30% 0.00% NA
All Indica  2759 86.20% 13.50% 0.36% 0.00% NA
All Japonica  1512 99.70% 0.20% 0.13% 0.00% NA
Aus  269 49.10% 50.20% 0.74% 0.00% NA
Indica I  595 86.90% 13.10% 0.00% 0.00% NA
Indica II  465 79.80% 19.80% 0.43% 0.00% NA
Indica III  913 87.00% 12.40% 0.66% 0.00% NA
Indica Intermediate  786 88.40% 11.30% 0.25% 0.00% NA
Temperate Japonica  767 99.50% 0.30% 0.26% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 92.20% 7.80% 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
vg0225615391 G -> A LOC_Os02g42590.1 upstream_gene_variant ; 3630.0bp to feature; MODIFIER silent_mutation Average:76.431; most accessible tissue: Minghui63 panicle, score: 90.184 N N N N
vg0225615391 G -> A LOC_Os02g42590.3 upstream_gene_variant ; 3630.0bp to feature; MODIFIER silent_mutation Average:76.431; most accessible tissue: Minghui63 panicle, score: 90.184 N N N N
vg0225615391 G -> A LOC_Os02g42590.2 upstream_gene_variant ; 3630.0bp to feature; MODIFIER silent_mutation Average:76.431; most accessible tissue: Minghui63 panicle, score: 90.184 N N N N
vg0225615391 G -> A LOC_Os02g42585-LOC_Os02g42590 intergenic_region ; MODIFIER silent_mutation Average:76.431; most accessible tissue: Minghui63 panicle, score: 90.184 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225615391 6.57E-08 NA mr1067 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
vg0225615391 NA 2.73E-06 mr1072 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