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Detailed information for vg0212510929:

Variant ID: vg0212510929 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 12510929
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


TGAGATCGTGCTAGCCGACAGGTCAGTTAATGTTGCTAGTGTCAATTTAGCTCTTTGGGAGATGGATGGGATTGATTGCCTGTCTGGAAAAGTTTGGGAT[G/A]
GAGATTTTCTAAAAGTGTCCGATTGTGATATACAGCCAATTGAAGATGGAGACCCCAAATTATTATTTTAAGGGCGTCGTGCAGGGTTCAAATTTCTACA

Reverse complement sequence

TGTAGAAATTTGAACCCTGCACGACGCCCTTAAAATAATAATTTGGGGTCTCCATCTTCAATTGGCTGTATATCACAATCGGACACTTTTAGAAAATCTC[C/T]
ATCCCAAACTTTTCCAGACAGGCAATCAATCCCATCCATCTCCCAAAGAGCTAAATTGACACTAGCAACATTAACTGACCTGTCGGCTAGCACGATCTCA

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 99.40% 0.40% 0.21% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 98.30% 1.10% 0.66% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 97.30% 1.60% 1.17% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 1.70% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0212510929 G -> A LOC_Os02g21090.1 upstream_gene_variant ; 4042.0bp to feature; MODIFIER silent_mutation Average:45.889; most accessible tissue: Minghui63 flag leaf, score: 69.681 N N N N
vg0212510929 G -> A LOC_Os02g21090.3 upstream_gene_variant ; 4792.0bp to feature; MODIFIER silent_mutation Average:45.889; most accessible tissue: Minghui63 flag leaf, score: 69.681 N N N N
vg0212510929 G -> A LOC_Os02g21090.2 upstream_gene_variant ; 3820.0bp to feature; MODIFIER silent_mutation Average:45.889; most accessible tissue: Minghui63 flag leaf, score: 69.681 N N N N
vg0212510929 G -> A LOC_Os02g21100.1 intron_variant ; MODIFIER silent_mutation Average:45.889; most accessible tissue: Minghui63 flag leaf, score: 69.681 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0212510929 1.29E-07 2.42E-13 Awn_length Jap_All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0212510929 2.25E-07 4.15E-06 mr1446 Jap_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
vg0212510929 NA 9.46E-06 mr1038_2 Jap_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