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Detailed information for vg0224495790:

Variant ID: vg0224495790 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24495790
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


ACATAGCAGGAAATAGGCATGAGTGGCTTTAATAAACAAGGATCACAGGTACTGAGAAAAAAGACAATGCTAAACACAAGTACCTAGCACGAAGGATAGC[G/A,T]
CTGCGATCATTCTTTGCCGTGTCAGCTATAAGTGGAAGAATACGTGAAACCTTGCAGTTCCGCAGGATCTGAAAGACAATAATTGTCAAAAAGAAAAATG

Reverse complement sequence

CATTTTTCTTTTTGACAATTATTGTCTTTCAGATCCTGCGGAACTGCAAGGTTTCACGTATTCTTCCACTTATAGCTGACACGGCAAAGAATGATCGCAG[C/T,A]
GCTATCCTTCGTGCTAGGTACTTGTGTTTAGCATTGTCTTTTTTCTCAGTACCTGTGATCCTTGTTTATTAAAGCCACTCATGCCTATTTCCTGCTATGT

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 78.20% 21.70% 0.02% 0.00% T: 0.02%
All Indica  2759 71.80% 28.10% 0.04% 0.00% T: 0.04%
All Japonica  1512 86.00% 14.00% 0.00% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 57.80% 42.20% 0.00% 0.00% NA
Indica II  465 69.90% 29.90% 0.22% 0.00% NA
Indica III  913 80.60% 19.30% 0.00% 0.00% T: 0.11%
Indica Intermediate  786 73.30% 26.70% 0.00% 0.00% NA
Temperate Japonica  767 83.30% 16.70% 0.00% 0.00% NA
Tropical Japonica  504 88.90% 11.10% 0.00% 0.00% NA
Japonica Intermediate  241 88.40% 11.60% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0224495790 G -> A LOC_Os02g40430.1 synonymous_variant ; p.Ser156Ser; LOW synonymous_codon Average:53.244; most accessible tissue: Callus, score: 81.043 N N N N
vg0224495790 G -> T LOC_Os02g40430.1 missense_variant ; p.Ser156Arg; MODERATE nonsynonymous_codon ; S156R Average:53.244; most accessible tissue: Callus, score: 81.043 possibly damaging 1.782 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224495790 1.51E-06 1.51E-06 mr1487 Ind_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