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Detailed information for vg0314510532:

Variant ID: vg0314510532 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14510532
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: 309. )

Flanking Sequence (100 bp) in Reference Genome:


TGATAATATGATTTAGACAGAAGAGATGTTCCATTGAGCTCATCATGTTTAAAGTGCTGATTGCTAAACAAATGTTTTCAGAATATGTTCTTCCCTGTCT[G/A]
CTATCTCTGAAGTGATGAAATGGTTGTATTAGCTTACGAGCTAAACGAGCTAGCTCGAGCCAACTCGAGCTAGCTGGCTCGTTAACCTACCGAGCCAGAG

Reverse complement sequence

CTCTGGCTCGGTAGGTTAACGAGCCAGCTAGCTCGAGTTGGCTCGAGCTAGCTCGTTTAGCTCGTAAGCTAATACAACCATTTCATCACTTCAGAGATAG[C/T]
AGACAGGGAAGAACATATTCTGAAAACATTTGTTTAGCAATCAGCACTTTAAACATGATGAGCTCAATGGAACATCTCTTCTGTCTAAATCATATTATCA

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 97.50% 1.40% 1.06% 0.00% NA
All Indica  2759 95.80% 2.40% 1.78% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 86.70% 8.20% 5.04% 0.00% NA
Indica II  465 99.40% 0.20% 0.43% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 95.90% 2.00% 2.04% 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 98.90% 1.10% 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
vg0314510532 G -> A LOC_Os03g25374.1 upstream_gene_variant ; 1970.0bp to feature; MODIFIER silent_mutation Average:41.666; most accessible tissue: Callus, score: 67.47 N N N N
vg0314510532 G -> A LOC_Os03g25380.1 upstream_gene_variant ; 1948.0bp to feature; MODIFIER silent_mutation Average:41.666; most accessible tissue: Callus, score: 67.47 N N N N
vg0314510532 G -> A LOC_Os03g25370.1 downstream_gene_variant ; 4559.0bp to feature; MODIFIER silent_mutation Average:41.666; most accessible tissue: Callus, score: 67.47 N N N N
vg0314510532 G -> A LOC_Os03g25390.2 downstream_gene_variant ; 3164.0bp to feature; MODIFIER silent_mutation Average:41.666; most accessible tissue: Callus, score: 67.47 N N N N
vg0314510532 G -> A LOC_Os03g25390.1 downstream_gene_variant ; 3164.0bp to feature; MODIFIER silent_mutation Average:41.666; most accessible tissue: Callus, score: 67.47 N N N N
vg0314510532 G -> A LOC_Os03g25390.3 downstream_gene_variant ; 3164.0bp to feature; MODIFIER silent_mutation Average:41.666; most accessible tissue: Callus, score: 67.47 N N N N
vg0314510532 G -> A LOC_Os03g25374-LOC_Os03g25380 intergenic_region ; MODIFIER silent_mutation Average:41.666; most accessible tissue: Callus, score: 67.47 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314510532 NA 7.06E-08 mr1542 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
vg0314510532 9.41E-09 6.74E-11 mr1542_2 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