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Detailed information for vg0208009640:

Variant ID: vg0208009640 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8009640
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GAGTTTGTCTGGCCTGCTTCTTTTTATATAGGAGTGAAGGCACGATTGAATAGAGCAAGCAGAAGTTAGAATCTAATCTCTCCCCCTCTCTGTTTCCTAT[G/A]
TTCCACCACGGCACCTGGGAAGCGAGGGCTCTGGCCTCGCTCTTCTCGCTCTTCTGTCGGTCGAGCACAGCTACCACTGAGGCATTCGGGCCCTCCCCAG

Reverse complement sequence

CTGGGGAGGGCCCGAATGCCTCAGTGGTAGCTGTGCTCGACCGACAGAAGAGCGAGAAGAGCGAGGCCAGAGCCCTCGCTTCCCAGGTGCCGTGGTGGAA[C/T]
ATAGGAAACAGAGAGGGGGAGAGATTAGATTCTAACTTCTGCTTGCTCTATTCAATCGTGCCTTCACTCCTATATAAAAAGAAGCAGGCCAGACAAACTC

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 96.60% 2.90% 0.51% 0.00% NA
All Indica  2759 99.10% 0.80% 0.07% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.07% 0.00% NA
Aus  269 69.90% 24.20% 5.95% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 98.50% 1.30% 0.25% 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 98.80% 0.80% 0.41% 0.00% NA
VI/Aromatic  96 54.20% 41.70% 4.17% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg0208009640 G -> A LOC_Os02g14530.1 intron_variant ; MODIFIER silent_mutation Average:53.517; most accessible tissue: Zhenshan97 young leaf, score: 80.589 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208009640 NA 4.14E-09 mr1570 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
vg0208009640 NA 7.32E-09 mr1057_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
vg0208009640 NA 7.36E-07 mr1126_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
vg0208009640 NA 7.33E-08 mr1567_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
vg0208009640 NA 1.42E-12 mr1612_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
vg0208009640 NA 5.98E-06 mr1976_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