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Detailed information for vg0431162265:

Variant ID: vg0431162265 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31162265
Reference Allele: GAlternative Allele: A,C
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, A: 0.23, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


CCTGATCTGATATTGTCAGTTTCATATTATTTGGTCACTTCTCTTTCCAATCACATTGATATATACTATCTTATCTCCATTTTAGGTTATAAAATATTTT[G/A,C]
ACTTTGGTCAAAGTGAAACTGTTTCAATAATTGAATATATTTTTATAATAAATTTGTTTTGAGTTGAAAATATTACTATTTTTTTCTACAAACCTAGTCA

Reverse complement sequence

TGACTAGGTTTGTAGAAAAAAATAGTAATATTTTCAACTCAAAACAAATTTATTATAAAAATATATTCAATTATTGAAACAGTTTCACTTTGACCAAAGT[C/T,G]
AAAATATTTTATAACCTAAAATGGAGATAAGATAGTATATATCAATGTGATTGGAAAGAGAAGTGACCAAATAATATGAAACTGACAATATCAGATCAGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.80% 44.10% 0.08% 0.00% C: 0.02%
All Indica  2759 79.40% 20.40% 0.14% 0.00% NA
All Japonica  1512 20.30% 79.70% 0.00% 0.00% NA
Aus  269 17.50% 82.50% 0.00% 0.00% NA
Indica I  595 88.20% 11.30% 0.50% 0.00% NA
Indica II  465 81.70% 18.30% 0.00% 0.00% NA
Indica III  913 73.30% 26.70% 0.00% 0.00% NA
Indica Intermediate  786 78.60% 21.20% 0.13% 0.00% NA
Temperate Japonica  767 22.90% 77.10% 0.00% 0.00% NA
Tropical Japonica  504 7.50% 92.50% 0.00% 0.00% NA
Japonica Intermediate  241 38.60% 61.40% 0.00% 0.00% NA
VI/Aromatic  96 43.80% 56.20% 0.00% 0.00% NA
Intermediate  90 52.20% 46.70% 0.00% 0.00% C: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0431162265 G -> C LOC_Os04g52420-LOC_Os04g52440 intergenic_region ; MODIFIER silent_mutation Average:65.675; most accessible tissue: Callus, score: 82.241 N N N N
vg0431162265 G -> A LOC_Os04g52420-LOC_Os04g52440 intergenic_region ; MODIFIER silent_mutation Average:65.675; most accessible tissue: Callus, score: 82.241 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431162265 8.23E-08 NA mr1790_2 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
vg0431162265 2.82E-08 NA mr1805_2 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
vg0431162265 NA 3.26E-07 mr1805_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
vg0431162265 4.14E-06 NA mr1805_2 Jap_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