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Detailed information for vg0101295924:

Variant ID: vg0101295924 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 1295924
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.82, G: 0.18, others allele: 0.00, population size: 51. )

Flanking Sequence (100 bp) in Reference Genome:


AGAATTTAGCCACAAGATGACCCACATAGAATGGAAAAATAATTGTTTCATCTCTTGTTCATAAAGTGAATGAGAGAGAAAAAATATTTTCTTTTTGCTT[A/G]
TGGTAGAACTTAAGCATAAGATGCACCCTAAGCTAATGCTACTTTCCACAATGTATATGGCTCACTTTACAAGTGCAATCATTGTCTTAAGGTCATCTTT

Reverse complement sequence

AAAGATGACCTTAAGACAATGATTGCACTTGTAAAGTGAGCCATATACATTGTGGAAAGTAGCATTAGCTTAGGGTGCATCTTATGCTTAAGTTCTACCA[T/C]
AAGCAAAAAGAAAATATTTTTTCTCTCTCATTCACTTTATGAACAAGAGATGAAACAATTATTTTTCCATTCTATGTGGGTCATCTTGTGGCTAAATTCT

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 74.80% 7.40% 0.38% 17.46% NA
All Indica  2759 70.20% 2.80% 0.62% 26.31% NA
All Japonica  1512 93.60% 0.30% 0.00% 6.08% NA
Aus  269 11.90% 87.40% 0.00% 0.74% NA
Indica I  595 77.30% 0.00% 1.01% 21.68% NA
Indica II  465 95.70% 0.20% 0.00% 4.09% NA
Indica III  913 53.10% 3.20% 0.77% 42.94% NA
Indica Intermediate  786 69.70% 6.10% 0.51% 23.66% NA
Temperate Japonica  767 88.10% 0.10% 0.00% 11.73% NA
Tropical Japonica  504 99.00% 0.60% 0.00% 0.40% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 81.20% 16.70% 1.04% 1.04% NA
Intermediate  90 80.00% 15.60% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0101295924 A -> G LOC_Os01g03210-LOC_Os01g03220 intergenic_region ; MODIFIER silent_mutation Average:50.267; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N
vg0101295924 A -> DEL N N silent_mutation Average:50.267; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0101295924 2.55E-06 NA mr1148_2 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
vg0101295924 9.16E-07 NA mr1256_2 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
vg0101295924 NA 5.01E-06 mr1574_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
vg0101295924 NA 1.05E-08 mr1762_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