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Detailed information for vg0425698075:

Variant ID: vg0425698075 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 25698075
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.89, G: 0.11, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGTGTGAGCTTCCTCATTGATCTTGATTGATTGTGTGCATATGCATTACTTCATATCCATATATATGCACATCTTGAGGGGGAGCTTATTCTATATTT[G/T]
GTTCATTATAAGATCTCTACCTTGATTTGAAATTATCTTTCATCTCATCTCTTTGTATTGTTTATATCGGATTATTATCTATCACAAAAGAGAGAAAAGA

Reverse complement sequence

TCTTTTCTCTCTTTTGTGATAGATAATAATCCGATATAAACAATACAAAGAGATGAGATGAAAGATAATTTCAAATCAAGGTAGAGATCTTATAATGAAC[C/A]
AAATATAGAATAAGCTCCCCCTCAAGATGTGCATATATATGGATATGAAGTAATGCATATGCACACAATCAATCAAGATCAATGAGGAAGCTCACACTAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.50% 8.50% 0.00% 0.00% NA
All Indica  2759 90.60% 9.40% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 50.90% 49.10% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 78.50% 21.50% 0.00% 0.00% NA
Indica Intermediate  786 93.10% 6.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0425698075 G -> T LOC_Os04g43410.1 upstream_gene_variant ; 4157.0bp to feature; MODIFIER silent_mutation Average:26.662; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N
vg0425698075 G -> T LOC_Os04g43420.1 upstream_gene_variant ; 2786.0bp to feature; MODIFIER silent_mutation Average:26.662; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N
vg0425698075 G -> T LOC_Os04g43430.1 downstream_gene_variant ; 3999.0bp to feature; MODIFIER silent_mutation Average:26.662; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N
vg0425698075 G -> T LOC_Os04g43430.2 downstream_gene_variant ; 3999.0bp to feature; MODIFIER silent_mutation Average:26.662; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N
vg0425698075 G -> T LOC_Os04g43410-LOC_Os04g43420 intergenic_region ; MODIFIER silent_mutation Average:26.662; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0425698075 NA 2.83E-06 mr1705 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
vg0425698075 4.24E-06 NA mr1580_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