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Detailed information for vg0915673890:

Variant ID: vg0915673890 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 15673890
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, G: 0.08, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


GCGAGCAGTAGAGGATAATAATGTGTTTTTCTTACCGGAAAAAGAAAACAATAAGGTTGAGGATAAGTAAAATATTTATATTAGGTGAGTAGCTATATTT[A/G]
TGACGCCATATTTTTCACCAAAAAATAGTCGGTATGTATTTACATTGTAAGTCCCTAAATTACATATGTATTTTTAGTGTATTTTCAATGTAAGTCCCAA

Reverse complement sequence

TTGGGACTTACATTGAAAATACACTAAAAATACATATGTAATTTAGGGACTTACAATGTAAATACATACCGACTATTTTTTGGTGAAAAATATGGCGTCA[T/C]
AAATATAGCTACTCACCTAATATAAATATTTTACTTATCCTCAACCTTATTGTTTTCTTTTTCCGGTAAGAAAAACACATTATTATCCTCTACTGCTCGC

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 55.20% 44.40% 0.17% 0.19% NA
All Indica  2759 27.60% 71.80% 0.25% 0.33% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 68.00% 32.00% 0.00% 0.00% NA
Indica I  595 37.80% 61.70% 0.17% 0.34% NA
Indica II  465 14.20% 85.20% 0.43% 0.22% NA
Indica III  913 24.40% 75.10% 0.00% 0.44% NA
Indica Intermediate  786 31.40% 67.80% 0.51% 0.25% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 75.60% 23.30% 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
vg0915673890 A -> G LOC_Os09g26050-LOC_Os09g26060 intergenic_region ; MODIFIER silent_mutation Average:50.676; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0915673890 A -> DEL N N silent_mutation Average:50.676; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0915673890 NA 7.17E-06 mr1011 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
vg0915673890 NA 8.00E-07 mr1707 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
vg0915673890 NA 3.52E-06 mr1728 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
vg0915673890 NA 5.27E-06 mr1006_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
vg0915673890 NA 8.98E-07 mr1707_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
vg0915673890 NA 5.07E-09 mr1728_2 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
vg0915673890 NA 2.62E-09 mr1860_2 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
vg0915673890 NA 2.90E-06 mr1974_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