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Detailed information for vg0825346100:

Variant ID: vg0825346100 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25346100
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


ATGCAAATGATGCCTATTCAACCCAGTGTCACCATGTGGGGAAGCATGATGAATGGTTGCAAGGTACATGGCAGGGCTGATATTGCTGAGAGGGTAGGAA[G/A]
GCAGGTTGCTGAGCTTAATCCTCAGTTTGGCGCAATATATGTGATAATGTCCAATATATATGCGGAGATTGGTAGGTGGCATGCAGTGGAGCACACCAGG

Reverse complement sequence

CCTGGTGTGCTCCACTGCATGCCACCTACCAATCTCCGCATATATATTGGACATTATCACATATATTGCGCCAAACTGAGGATTAAGCTCAGCAACCTGC[C/T]
TTCCTACCCTCTCAGCAATATCAGCCCTGCCATGTACCTTGCAACCATTCATCATGCTTCCCCACATGGTGACACTGGGTTGAATAGGCATCATTTGCAT

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 94.90% 5.10% 0.00% 0.00% NA
All Indica  2759 97.90% 2.10% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 33.80% 66.20% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 96.20% 3.80% 0.00% 0.00% NA
Indica Intermediate  786 97.30% 2.70% 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 96.90% 3.10% 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
vg0825346100 G -> A LOC_Os08g40020.1 missense_variant ; p.Arg455Lys; MODERATE nonsynonymous_codon ; R455K Average:62.299; most accessible tissue: Callus, score: 69.474 unknown unknown TOLERATED 0.43

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825346100 NA 7.36E-06 mr1349 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
vg0825346100 NA 7.03E-12 mr1918_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