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Detailed information for vg0327296764:

Variant ID: vg0327296764 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 27296764
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TGAGAAAAAACTCTATAAAACTACCACTAGAAATTTTTTGTTACATTAACCACCATTGAAATTGGCCTAAGAGCAATTTCAATAGAAGAGTAAGCCGTCA[G/A]
CTCTAAAACCTATCAAACACATAGAGTGCTGCTCCACCAAACAGATATCATGTACAACAAAAGTCTACAAGCTTGCCATCACGCAATTACCAAAGTCTTT

Reverse complement sequence

AAAGACTTTGGTAATTGCGTGATGGCAAGCTTGTAGACTTTTGTTGTACATGATATCTGTTTGGTGGAGCAGCACTCTATGTGTTTGATAGGTTTTAGAG[C/T]
TGACGGCTTACTCTTCTATTGAAATTGCTCTTAGGCCAATTTCAATGGTGGTTAATGTAACAAAAAATTTCTAGTGGTAGTTTTATAGAGTTTTTTCTCA

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 96.70% 2.10% 1.29% 0.00% NA
All Indica  2759 94.50% 3.30% 2.17% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.60% 0.00% 3.36% 0.00% NA
Indica II  465 77.20% 17.20% 5.59% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 96.80% 1.40% 1.78% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 95.60% 3.30% 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
vg0327296764 G -> A LOC_Os03g48010.1 upstream_gene_variant ; 584.0bp to feature; MODIFIER silent_mutation Average:63.956; most accessible tissue: Callus, score: 91.888 N N N N
vg0327296764 G -> A LOC_Os03g48000.1 downstream_gene_variant ; 2258.0bp to feature; MODIFIER silent_mutation Average:63.956; most accessible tissue: Callus, score: 91.888 N N N N
vg0327296764 G -> A LOC_Os03g48030.1 downstream_gene_variant ; 3963.0bp to feature; MODIFIER silent_mutation Average:63.956; most accessible tissue: Callus, score: 91.888 N N N N
vg0327296764 G -> A LOC_Os03g48000.2 downstream_gene_variant ; 2395.0bp to feature; MODIFIER silent_mutation Average:63.956; most accessible tissue: Callus, score: 91.888 N N N N
vg0327296764 G -> A LOC_Os03g48000.3 downstream_gene_variant ; 2395.0bp to feature; MODIFIER silent_mutation Average:63.956; most accessible tissue: Callus, score: 91.888 N N N N
vg0327296764 G -> A LOC_Os03g48000-LOC_Os03g48010 intergenic_region ; MODIFIER silent_mutation Average:63.956; most accessible tissue: Callus, score: 91.888 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0327296764 1.45E-06 1.42E-06 mr1632 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