\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0314344500:

Variant ID: vg0314344500 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14344500
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, A: 0.08, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


GACATCCAATTAATACATACTAGCACAGTACTGTACTTGTGTGTCCTAAAACAAAAATATGTTTTATTCTACACATATAACATCAACCAAGGAAACATAA[T/A]
AGAGAAAAAGTTTGATTTGAAAGATATCTTTTCCATCATATTTTCCTATGCTGCAAGCTAGATGGATCTTCAAACCAATGGCGCCTCTATTAATTCAATA

Reverse complement sequence

TATTGAATTAATAGAGGCGCCATTGGTTTGAAGATCCATCTAGCTTGCAGCATAGGAAAATATGATGGAAAAGATATCTTTCAAATCAAACTTTTTCTCT[A/T]
TTATGTTTCCTTGGTTGATGTTATATGTGTAGAATAAAACATATTTTTGTTTTAGGACACACAAGTACAGTACTGTGCTAGTATGTATTAATTGGATGTC

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 50.00% 49.70% 0.11% 0.28% NA
All Indica  2759 79.70% 19.70% 0.11% 0.47% NA
All Japonica  1512 0.40% 99.60% 0.00% 0.00% NA
Aus  269 43.10% 56.50% 0.37% 0.00% NA
Indica I  595 64.20% 35.10% 0.00% 0.67% NA
Indica II  465 58.70% 40.20% 0.22% 0.86% NA
Indica III  913 95.50% 4.30% 0.11% 0.11% NA
Indica Intermediate  786 85.50% 13.90% 0.13% 0.51% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 0.40% 99.60% 0.00% 0.00% NA
VI/Aromatic  96 13.50% 86.50% 0.00% 0.00% NA
Intermediate  90 30.00% 68.90% 1.11% 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
vg0314344500 T -> A LOC_Os03g25110.1 downstream_gene_variant ; 2792.0bp to feature; MODIFIER silent_mutation Average:45.543; most accessible tissue: Callus, score: 87.266 N N N N
vg0314344500 T -> A LOC_Os03g25120.1 intron_variant ; MODIFIER silent_mutation Average:45.543; most accessible tissue: Callus, score: 87.266 N N N N
vg0314344500 T -> DEL N N silent_mutation Average:45.543; most accessible tissue: Callus, score: 87.266 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314344500 NA 2.38E-06 mr1094 Ind_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
vg0314344500 NA 1.87E-08 mr1514 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
vg0314344500 4.44E-09 NA mr1542 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
vg0314344500 7.65E-08 1.00E-11 mr1542 Ind_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
vg0314344500 NA 3.70E-07 mr1877 Ind_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
vg0314344500 NA 6.23E-06 mr1929 Ind_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
vg0314344500 8.67E-11 NA mr1542_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
vg0314344500 2.04E-10 2.15E-14 mr1542_2 Ind_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
vg0314344500 4.48E-08 NA mr1587_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
vg0314344500 NA 9.84E-06 mr1587_2 Ind_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
vg0314344500 NA 1.11E-07 mr1877_2 Ind_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