Search for Variation information by Variation ID:

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

Detailed information for vg0321293433:

Variant ID: vg0321293433 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21293433
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TTCCTGATCTGTTATGCAACTATGCCTGGCATCTTTTCTGACATGTTCAAGGCATTTGTAGATAGGGACTAGTGCAACACATGGTTTCAGGTGTGGTTAT[C/T]
TCCATGGCAGTGTAGAATGGCATGGAATGTTTGTTCATCAATATGTTTCGTGATATGGTGTGGGTTCGTGTATATCTTGCTTGCTTGCTCTCGGAAGTCT

Reverse complement sequence

AGACTTCCGAGAGCAAGCAAGCAAGATATACACGAACCCACACCATATCACGAAACATATTGATGAACAAACATTCCATGCCATTCTACACTGCCATGGA[G/A]
ATAACCACACCTGAAACCATGTGTTGCACTAGTCCCTATCTACAAATGCCTTGAACATGTCAGAAAAGATGCCAGGCATAGTTGCATAACAGATCAGGAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.20% 4.80% 0.06% 0.00% NA
All Indica  2759 99.20% 0.70% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 24.20% 75.10% 0.74% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.60% 0.30% 0.11% 0.00% NA
Indica Intermediate  786 97.80% 2.20% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0321293433 C -> T LOC_Os03g38359.1 downstream_gene_variant ; 4309.0bp to feature; MODIFIER silent_mutation Average:64.776; most accessible tissue: Callus, score: 93.632 N N N N
vg0321293433 C -> T LOC_Os03g38359-LOC_Os03g38370 intergenic_region ; MODIFIER silent_mutation Average:64.776; most accessible tissue: Callus, score: 93.632 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321293433 3.41E-07 NA mr1116 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
vg0321293433 2.17E-07 NA mr1242 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
vg0321293433 8.36E-06 NA mr1496 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
vg0321293433 9.59E-07 NA mr1118_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
vg0321293433 5.03E-07 NA mr1242_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
vg0321293433 2.11E-06 NA mr1496_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
vg0321293433 NA 6.18E-27 mr1757_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
vg0321293433 NA 1.03E-06 mr1762_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