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Detailed information for vg0404806537:

Variant ID: vg0404806537 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 4806537
Reference Allele: AAlternative Allele: G,C
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:


CACGTGGCAATCCAGTCAGCATTTTATTTTTTAAAAAATAGTGGGACCCACTTGTCATACCATATCTTCCCCTCTTCCTTTTCCTCTCTCTCAGGCTCAG[A/G,C]
GCGTGCACGGCGAGCGGCGGCGCGCGGGGGAGGACAGGCAGTCGGTGCGCGGGGGCCGGCGATGGGCGGTGACGTGCTGGGGCGGACGGGCGGTCGGCGC

Reverse complement sequence

GCGCCGACCGCCCGTCCGCCCCAGCACGTCACCGCCCATCGCCGGCCCCCGCGCACCGACTGCCTGTCCTCCCCCGCGCGCCGCCGCTCGCCGTGCACGC[T/C,G]
CTGAGCCTGAGAGAGAGGAAAAGGAAGAGGGGAAGATATGGTATGACAAGTGGGTCCCACTATTTTTTAAAAAATAAAATGCTGACTGGATTGCCACGTG

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 78.30% 9.60% 1.33% 10.73% C: 0.02%
All Indica  2759 79.40% 3.70% 0.80% 16.09% NA
All Japonica  1512 72.80% 22.70% 2.65% 1.85% C: 0.07%
Aus  269 88.50% 0.40% 0.00% 11.15% NA
Indica I  595 99.00% 0.70% 0.17% 0.17% NA
Indica II  465 78.50% 8.00% 1.29% 12.26% NA
Indica III  913 68.50% 2.30% 0.77% 28.48% NA
Indica Intermediate  786 77.70% 5.20% 1.02% 16.03% NA
Temperate Japonica  767 85.10% 14.00% 0.52% 0.26% C: 0.13%
Tropical Japonica  504 63.70% 25.20% 6.75% 4.37% NA
Japonica Intermediate  241 52.30% 45.20% 0.83% 1.66% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 84.40% 8.90% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0404806537 A -> C LOC_Os04g08792.1 upstream_gene_variant ; 2118.0bp to feature; MODIFIER silent_mutation Average:67.305; most accessible tissue: Zhenshan97 flag leaf, score: 83.684 N N N N
vg0404806537 A -> C LOC_Os04g08796.1 upstream_gene_variant ; 4087.0bp to feature; MODIFIER silent_mutation Average:67.305; most accessible tissue: Zhenshan97 flag leaf, score: 83.684 N N N N
vg0404806537 A -> C LOC_Os04g08792-LOC_Os04g08796 intergenic_region ; MODIFIER silent_mutation Average:67.305; most accessible tissue: Zhenshan97 flag leaf, score: 83.684 N N N N
vg0404806537 A -> DEL N N silent_mutation Average:67.305; most accessible tissue: Zhenshan97 flag leaf, score: 83.684 N N N N
vg0404806537 A -> G LOC_Os04g08792.1 upstream_gene_variant ; 2118.0bp to feature; MODIFIER silent_mutation Average:67.305; most accessible tissue: Zhenshan97 flag leaf, score: 83.684 N N N N
vg0404806537 A -> G LOC_Os04g08796.1 upstream_gene_variant ; 4087.0bp to feature; MODIFIER silent_mutation Average:67.305; most accessible tissue: Zhenshan97 flag leaf, score: 83.684 N N N N
vg0404806537 A -> G LOC_Os04g08792-LOC_Os04g08796 intergenic_region ; MODIFIER silent_mutation Average:67.305; most accessible tissue: Zhenshan97 flag leaf, score: 83.684 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0404806537 4.22E-07 NA mr1679 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
vg0404806537 2.10E-07 NA mr1693 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
vg0404806537 3.77E-06 NA mr1693 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
vg0404806537 4.93E-06 NA mr1720 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