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Detailed information for vg0709586016:

Variant ID: vg0709586016 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 9586016
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, A: 0.13, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


GCAAACAACAAATGGTTTGTGGTGTTTTGTGAACCAAATCCAAAAAGCATCTTCAACGCCAAAAAATTTCAAAGAAAAATCTCTCACTTTCGAAAAGAAA[G/A]
AGATTCCTTCTACTTATGACAATAATGCACAATTTGTTACCTTGTTCTCCCCCTTTTGACAATGAGTTCATCAAAATTTTTTTCCTCGGAGAGCTTTGCT

Reverse complement sequence

AGCAAAGCTCTCCGAGGAAAAAAATTTTGATGAACTCATTGTCAAAAGGGGGAGAACAAGGTAACAAATTGTGCATTATTGTCATAAGTAGAAGGAATCT[C/T]
TTTCTTTTCGAAAGTGAGAGATTTTTCTTTGAAATTTTTTGGCGTTGAAGATGCTTTTTGGATTTGGTTCACAAAACACCACAAACCATTTGTTGTTTGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.90% 6.10% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 81.60% 18.40% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 74.60% 25.40% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 67.60% 32.40% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0709586016 G -> A LOC_Os07g16400.1 upstream_gene_variant ; 3498.0bp to feature; MODIFIER silent_mutation Average:25.113; most accessible tissue: Callus, score: 50.199 N N N N
vg0709586016 G -> A LOC_Os07g16380-LOC_Os07g16400 intergenic_region ; MODIFIER silent_mutation Average:25.113; most accessible tissue: Callus, score: 50.199 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0709586016 NA 5.92E-09 mr1624 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
vg0709586016 NA 1.79E-10 mr1624_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
vg0709586016 5.82E-07 NA mr1733_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
vg0709586016 NA 2.20E-09 mr1733_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
vg0709586016 NA 1.32E-06 mr1736_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
vg0709586016 NA 7.01E-11 mr1741_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
vg0709586016 NA 4.76E-07 mr1741_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
vg0709586016 NA 9.47E-06 mr1757_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
vg0709586016 NA 2.59E-06 mr1785_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