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Detailed information for vg0423711696:

Variant ID: vg0423711696 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 23711696
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: 0.01, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


TAAATTATTTATCTGATCATACCGTTGTGTTAATTATAACTAAATCTTTATAATAGGATATCACATGATTATATTCTGATAAGACAAAACATATGTTTCC[G/A]
TCCGATAACACTCAATGTTTTATATGCGATAGCATTATGTTTCAACGTGTATCTTTGTTGTGTTTCACATAATTTTTAAATGTTTCATTAGCTGATTTTT

Reverse complement sequence

AAAAATCAGCTAATGAAACATTTAAAAATTATGTGAAACACAACAAAGATACACGTTGAAACATAATGCTATCGCATATAAAACATTGAGTGTTATCGGA[C/T]
GGAAACATATGTTTTGTCTTATCAGAATATAATCATGTGATATCCTATTATAAAGATTTAGTTATAATTAACACAACGGTATGATCAGATAAATAATTTA

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 97.10% 2.70% 0.21% 0.00% NA
All Indica  2759 99.40% 0.60% 0.00% 0.00% NA
All Japonica  1512 92.70% 6.70% 0.60% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 80.20% 18.50% 1.39% 0.00% NA
Japonica Intermediate  241 95.90% 3.70% 0.41% 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
vg0423711696 G -> A LOC_Os04g39780.1 upstream_gene_variant ; 4348.0bp to feature; MODIFIER silent_mutation Average:27.324; most accessible tissue: Callus, score: 67.209 N N N N
vg0423711696 G -> A LOC_Os04g39800.1 upstream_gene_variant ; 1273.0bp to feature; MODIFIER silent_mutation Average:27.324; most accessible tissue: Callus, score: 67.209 N N N N
vg0423711696 G -> A LOC_Os04g39814.1 downstream_gene_variant ; 3750.0bp to feature; MODIFIER silent_mutation Average:27.324; most accessible tissue: Callus, score: 67.209 N N N N
vg0423711696 G -> A LOC_Os04g39814.2 downstream_gene_variant ; 3747.0bp to feature; MODIFIER silent_mutation Average:27.324; most accessible tissue: Callus, score: 67.209 N N N N
vg0423711696 G -> A LOC_Os04g39814.3 downstream_gene_variant ; 3747.0bp to feature; MODIFIER silent_mutation Average:27.324; most accessible tissue: Callus, score: 67.209 N N N N
vg0423711696 G -> A LOC_Os04g39800-LOC_Os04g39814 intergenic_region ; MODIFIER silent_mutation Average:27.324; most accessible tissue: Callus, score: 67.209 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0423711696 NA 2.76E-12 Grain_width Jap_All Not 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
vg0423711696 2.43E-06 2.43E-06 mr1384 Jap_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
vg0423711696 NA 3.62E-07 mr1830 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
vg0423711696 NA 2.54E-06 mr1077_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