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Detailed information for vg0916428525:

Variant ID: vg0916428525 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 16428525
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


TTGAAATTTGAACAGATCTCCGCTAAATTCACAACAAAATCTGAAAGTTTTATTACCAGGATCCACCGCTAGGCCCCATTTAAGATAACTGAAATTGATG[A/G]
ATACGCTTATTTTTATAGCTATTTGAAACTATAAACAGATGAATTAACTAGTAATATGTTGAACAGTTGCTTTAGAAAAAATATTTTATAAAACGTATTA

Reverse complement sequence

TAATACGTTTTATAAAATATTTTTTCTAAAGCAACTGTTCAACATATTACTAGTTAATTCATCTGTTTATAGTTTCAAATAGCTATAAAAATAAGCGTAT[T/C]
CATCAATTTCAGTTATCTTAAATGGGGCCTAGCGGTGGATCCTGGTAATAAAACTTTCAGATTTTGTTGTGAATTTAGCGGAGATCTGTTCAAATTTCAA

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 89.20% 10.80% 0.02% 0.00% NA
All Indica  2759 81.60% 18.40% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.50% 4.40% 0.17% 0.00% NA
Indica II  465 83.00% 17.00% 0.00% 0.00% NA
Indica III  913 70.60% 29.40% 0.00% 0.00% NA
Indica Intermediate  786 83.00% 17.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 0.00% 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
vg0916428525 A -> G LOC_Os09g27010.1 upstream_gene_variant ; 3307.0bp to feature; MODIFIER silent_mutation Average:85.537; most accessible tissue: Minghui63 young leaf, score: 93.766 N N N N
vg0916428525 A -> G LOC_Os09g27010-LOC_Os09g27020 intergenic_region ; MODIFIER silent_mutation Average:85.537; most accessible tissue: Minghui63 young leaf, score: 93.766 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0916428525 NA 7.04E-06 mr1064 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
vg0916428525 NA 1.23E-06 mr1534 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
vg0916428525 NA 2.19E-08 mr1671 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
vg0916428525 NA 2.24E-06 mr1741 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
vg0916428525 NA 5.68E-06 mr1870 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
vg0916428525 NA 3.33E-07 mr1951 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
vg0916428525 NA 1.33E-07 mr1671_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