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Detailed information for vg0235431697:

Variant ID: vg0235431697 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 35431697
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


CGCCAACAGTTTCGGGCACTCTGGCTGAACCCAAATCTGCAATACATACCAGCAATAAAGGATGTAGATTAAGTTGAGAATGAGGGACAAATAACCTGAG[A/T]
GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTCTTGGTTAAACTAATTACCTTTTCACTTCCGAAGTTGAGGTACAGGTCGCTTAT

Reverse complement sequence

ATAAGCGACCTGTACCTCAACTTCGGAAGTGAAAAGGTAATTAGTTTAACCAAGACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC[T/A]
CTCAGGTTATTTGTCCCTCATTCTCAACTTAATCTACATCCTTTATTGCTGGTATGTATTGCAGATTTGGGTTCAGCCAGAGTGCCCGAAACTGTTGGCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.50% 7.40% 5.08% 0.00% NA
All Indica  2759 96.80% 2.90% 0.33% 0.00% NA
All Japonica  1512 69.40% 16.00% 14.55% 0.00% NA
Aus  269 90.70% 6.70% 2.60% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 97.00% 2.40% 0.65% 0.00% NA
Indica III  913 95.20% 4.60% 0.22% 0.00% NA
Indica Intermediate  786 97.20% 2.30% 0.51% 0.00% NA
Temperate Japonica  767 71.20% 10.80% 17.99% 0.00% NA
Tropical Japonica  504 68.10% 22.80% 9.13% 0.00% NA
Japonica Intermediate  241 66.80% 18.30% 14.94% 0.00% NA
VI/Aromatic  96 94.80% 4.20% 1.04% 0.00% NA
Intermediate  90 88.90% 7.80% 3.33% 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
vg0235431697 A -> T LOC_Os02g57850.1 upstream_gene_variant ; 4356.0bp to feature; MODIFIER silent_mutation Average:79.802; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N
vg0235431697 A -> T LOC_Os02g57854.1 downstream_gene_variant ; 1057.0bp to feature; MODIFIER silent_mutation Average:79.802; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N
vg0235431697 A -> T LOC_Os02g57870.1 downstream_gene_variant ; 1965.0bp to feature; MODIFIER silent_mutation Average:79.802; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N
vg0235431697 A -> T LOC_Os02g57854.2 downstream_gene_variant ; 1057.0bp to feature; MODIFIER silent_mutation Average:79.802; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N
vg0235431697 A -> T LOC_Os02g57870.2 downstream_gene_variant ; 1898.0bp to feature; MODIFIER silent_mutation Average:79.802; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N
vg0235431697 A -> T LOC_Os02g57860.1 intron_variant ; MODIFIER silent_mutation Average:79.802; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0235431697 NA 8.35E-08 mr1354 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
vg0235431697 NA 4.89E-12 mr1871 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
vg0235431697 NA 1.70E-06 mr1418_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
vg0235431697 NA 3.11E-11 mr1680_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
vg0235431697 5.19E-07 1.44E-21 mr1968_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