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Detailed information for vg0517887899:

Variant ID: vg0517887899 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 17887899
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, T: 0.23, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTCCCTATCTAATTTATGAAACTTTCTGGACTAGCAAACGACAACAATTGACACCAGACAGATCTTACTAGCTCCCAAACAAGCCATTTGACTAAAAT[G/T]
TTCACTCTATGCCCATAAATATGGCACACTTTAGTGAGATGCAGATGCAGTTAATTTCAGAATCCAATAGGAGTAACAGAAAGTACCACCAAACATTGAA

Reverse complement sequence

TTCAATGTTTGGTGGTACTTTCTGTTACTCCTATTGGATTCTGAAATTAACTGCATCTGCATCTCACTAAAGTGTGCCATATTTATGGGCATAGAGTGAA[C/A]
ATTTTAGTCAAATGGCTTGTTTGGGAGCTAGTAAGATCTGTCTGGTGTCAATTGTTGTCGTTTGCTAGTCCAGAAAGTTTCATAAATTAGATAGGGACGG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.50% 35.40% 0.11% 0.00% NA
All Indica  2759 94.10% 5.80% 0.11% 0.00% NA
All Japonica  1512 8.70% 91.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 74.60% 25.20% 0.22% 0.00% NA
Indica III  913 99.10% 0.80% 0.11% 0.00% NA
Indica Intermediate  786 95.40% 4.50% 0.13% 0.00% NA
Temperate Japonica  767 3.10% 96.90% 0.00% 0.00% NA
Tropical Japonica  504 20.00% 80.00% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 52.20% 45.60% 2.22% 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
vg0517887899 G -> T LOC_Os05g30830.1 downstream_gene_variant ; 4070.0bp to feature; MODIFIER silent_mutation Average:63.065; most accessible tissue: Zhenshan97 flower, score: 76.751 N N N N
vg0517887899 G -> T LOC_Os05g30820.1 intron_variant ; MODIFIER silent_mutation Average:63.065; most accessible tissue: Zhenshan97 flower, score: 76.751 N N N N
vg0517887899 G -> T LOC_Os05g30820.2 intron_variant ; MODIFIER silent_mutation Average:63.065; most accessible tissue: Zhenshan97 flower, score: 76.751 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0517887899 NA 1.71E-06 mr1044 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
vg0517887899 NA 5.82E-06 mr1044 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
vg0517887899 NA 6.61E-12 mr1069 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
vg0517887899 NA 5.59E-19 mr1133 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
vg0517887899 NA 1.44E-29 mr1202 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
vg0517887899 NA 2.99E-12 mr1667 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
vg0517887899 NA 1.47E-17 mr1842 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
vg0517887899 NA 4.06E-12 mr1902 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
vg0517887899 NA 3.18E-39 mr1072_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
vg0517887899 NA 5.00E-07 mr1568_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
vg0517887899 NA 2.08E-07 mr1654_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
vg0517887899 NA 2.39E-14 mr1790_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
vg0517887899 NA 4.73E-22 mr1933_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