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Detailed information for vg0922500002:

Variant ID: vg0922500002 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 22500002
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.65, G: 0.35, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTCACAGATGAAGTTTCTTAAAAAAAAATTAAATAAATCGAATAAATTTGTTTCTAAAATTTATAATAGCTAATAGTTAATTAATCTTGTGCTAACG[G/A]
CTCATCTCGTATTCTTGTTTTTTTAAAAAAAAAAGCTCAATCCTCACAAAAGTAATTATTATTTTTTTTCCTATCATTTGATTCATTGTTAAATATACTT

Reverse complement sequence

AAGTATATTTAACAATGAATCAAATGATAGGAAAAAAAATAATAATTACTTTTGTGAGGATTGAGCTTTTTTTTTTAAAAAAACAAGAATACGAGATGAG[C/T]
CGTTAGCACAAGATTAATTAACTATTAGCTATTATAAATTTTAGAAACAAATTTATTCGATTTATTTAATTTTTTTTTAAGAAACTTCATCTGTGAAAAA

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 53.10% 46.70% 0.21% 0.00% NA
All Indica  2759 80.10% 19.60% 0.29% 0.00% NA
All Japonica  1512 0.60% 99.30% 0.07% 0.00% NA
Aus  269 92.20% 7.80% 0.00% 0.00% NA
Indica I  595 67.10% 32.60% 0.34% 0.00% NA
Indica II  465 90.50% 8.60% 0.86% 0.00% NA
Indica III  913 84.30% 15.70% 0.00% 0.00% NA
Indica Intermediate  786 79.00% 20.70% 0.25% 0.00% NA
Temperate Japonica  767 0.10% 99.70% 0.13% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 13.50% 86.50% 0.00% 0.00% NA
Intermediate  90 33.30% 65.60% 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
vg0922500002 G -> A LOC_Os09g39170-LOC_Os09g39180 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0922500002 NA 5.02E-10 mr1322 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
vg0922500002 NA 6.04E-11 mr1553 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
vg0922500002 5.25E-23 5.67E-85 mr1865 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
vg0922500002 2.23E-22 4.87E-24 mr1865 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
vg0922500002 NA 6.01E-07 mr1970 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
vg0922500002 NA 3.66E-07 mr1973 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
vg0922500002 NA 2.91E-13 mr1553_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
vg0922500002 1.19E-23 1.22E-96 mr1865_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
vg0922500002 5.57E-24 5.64E-27 mr1865_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
vg0922500002 NA 3.57E-06 mr1968_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
vg0922500002 NA 1.69E-07 mr1970_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