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Detailed information for vg0336260325:

Variant ID: vg0336260325 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 36260325
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.70, A: 0.30, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


CGTTGAAAGAAATGGCATGAAAGCGGTGGTGTTGCTGCTAGCTACTCCCTACATCCTAAAAAACCAACATAGCACCGGATATAACACATCATAATACTAC[G/A]
AATCTGAACATATATTTATCTAGATTTATAATACTAAAATGTATCACATCCATTTATTTTTTATGGGACGGAGGGAGCACTTTCTCCGTCCCATGCATAT

Reverse complement sequence

ATATGCATGGGACGGAGAAAGTGCTCCCTCCGTCCCATAAAAAATAAATGGATGTGATACATTTTAGTATTATAAATCTAGATAAATATATGTTCAGATT[C/T]
GTAGTATTATGATGTGTTATATCCGGTGCTATGTTGGTTTTTTAGGATGTAGGGAGTAGCTAGCAGCAACACCACCGCTTTCATGCCATTTCTTTCAACG

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 90.60% 9.10% 0.30% 0.00% NA
All Indica  2759 86.60% 13.00% 0.40% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 77.00% 22.70% 0.37% 0.00% NA
Indica I  595 91.80% 7.20% 1.01% 0.00% NA
Indica II  465 90.80% 9.20% 0.00% 0.00% NA
Indica III  913 80.90% 19.10% 0.00% 0.00% NA
Indica Intermediate  786 86.80% 12.60% 0.64% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 91.10% 6.70% 2.22% 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
vg0336260325 G -> A LOC_Os03g64170.1 upstream_gene_variant ; 826.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0336260325 G -> A LOC_Os03g64170.2 upstream_gene_variant ; 3006.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0336260325 G -> A LOC_Os03g64170-LOC_Os03g64190 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
vg0336260325 9.56E-06 1.76E-06 mr1285 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
vg0336260325 NA 2.60E-06 mr1285 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
vg0336260325 3.78E-06 3.78E-06 mr1501 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
vg0336260325 NA 2.59E-06 mr1909 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
vg0336260325 NA 7.21E-06 mr1982 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
vg0336260325 NA 2.80E-08 mr1654_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