Search for Variation information by Variation ID:

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

Detailed information for vg1224152951:

Variant ID: vg1224152951 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 24152951
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.82, A: 0.19, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


GTGATGTACTTATATATTCTAAATAGAAACCTAGAACAATCACGGTTGTTATTGTGGTCCGAAAAGAAAAAATATCAGACATTATTGCAGCTTGACATGC[G/A]
CAATATAGTGACCACTGATTTGTACAAAGGTTTGAAATTTCAAAGTTAAACATGTCATTTTCAATTTTTTAGAGATAATCCGAGAAATGCCATTGACAAG

Reverse complement sequence

CTTGTCAATGGCATTTCTCGGATTATCTCTAAAAAATTGAAAATGACATGTTTAACTTTGAAATTTCAAACCTTTGTACAAATCAGTGGTCACTATATTG[C/T]
GCATGTCAAGCTGCAATAATGTCTGATATTTTTTCTTTTCGGACCACAATAACAACCGTGATTGTTCTAGGTTTCTATTTAGAATATATAAGTACATCAC

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 92.00% 7.00% 0.95% 0.00% NA
All Indica  2759 86.90% 11.70% 1.41% 0.00% NA
All Japonica  1512 99.40% 0.30% 0.33% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.30% 0.20% 1.51% 0.00% NA
Indica II  465 71.60% 25.60% 2.80% 0.00% NA
Indica III  913 86.60% 12.70% 0.66% 0.00% NA
Indica Intermediate  786 87.70% 10.90% 1.40% 0.00% NA
Temperate Japonica  767 99.30% 0.30% 0.39% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.40% 0.83% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 4.40% 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
vg1224152951 G -> A LOC_Os12g39230.1 upstream_gene_variant ; 2438.0bp to feature; MODIFIER silent_mutation Average:32.575; most accessible tissue: Callus, score: 51.125 N N N N
vg1224152951 G -> A LOC_Os12g39300.1 downstream_gene_variant ; 1847.0bp to feature; MODIFIER silent_mutation Average:32.575; most accessible tissue: Callus, score: 51.125 N N N N
vg1224152951 G -> A LOC_Os12g39240.1 downstream_gene_variant ; 1985.0bp to feature; MODIFIER silent_mutation Average:32.575; most accessible tissue: Callus, score: 51.125 N N N N
vg1224152951 G -> A LOC_Os12g39230-LOC_Os12g39300 intergenic_region ; MODIFIER silent_mutation Average:32.575; most accessible tissue: Callus, score: 51.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1224152951 4.95E-06 NA mr1632 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
vg1224152951 NA 9.65E-06 mr1632 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