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Detailed information for vg0208432932:

Variant ID: vg0208432932 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8432932
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:


TGCACCTAATGTGAACATTTTAATTTGTAGGGAGAGGTACTATGGGCTTAACTTTCCTCGGTTGCCCAGCAACTTACCAACAACAATTCCAACAATTTTC[G/A]
CCTCAATGGCAAAGTGAAAGCCAAAAGTTTAGGGGCGAGCACCAAAAGATCTATCAATTTAGACAAGGAGATATTATTCCACTCCCAGCTGGTGTTGCAC

Reverse complement sequence

GTGCAACACCAGCTGGGAGTGGAATAATATCTCCTTGTCTAAATTGATAGATCTTTTGGTGCTCGCCCCTAAACTTTTGGCTTTCACTTTGCCATTGAGG[C/T]
GAAAATTGTTGGAATTGTTGTTGGTAAGTTGCTGGGCAACCGAGGAAAGTTAAGCCCATAGTACCTCTCCCTACAAATTAAAATGTTCACATTAGGTGCA

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 97.10% 2.10% 0.83% 0.00% NA
All Indica  2759 99.90% 0.00% 0.11% 0.00% NA
All Japonica  1512 91.10% 6.50% 2.38% 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 99.60% 0.00% 0.38% 0.00% NA
Temperate Japonica  767 85.80% 11.00% 3.26% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 89.60% 5.80% 4.56% 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
vg0208432932 G -> A LOC_Os02g15140.1 upstream_gene_variant ; 526.0bp to feature; MODIFIER silent_mutation Average:36.278; most accessible tissue: Zhenshan97 flower, score: 45.926 N N N N
vg0208432932 G -> A LOC_Os02g15130.1 downstream_gene_variant ; 3658.0bp to feature; MODIFIER silent_mutation Average:36.278; most accessible tissue: Zhenshan97 flower, score: 45.926 N N N N
vg0208432932 G -> A LOC_Os02g15130-LOC_Os02g15140 intergenic_region ; MODIFIER silent_mutation Average:36.278; most accessible tissue: Zhenshan97 flower, score: 45.926 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208432932 NA 5.00E-06 mr1045 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
vg0208432932 7.75E-06 1.02E-06 mr1236 Jap_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
vg0208432932 NA 3.99E-06 mr1318 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
vg0208432932 NA 1.26E-06 mr1531 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
vg0208432932 NA 2.89E-07 mr1629 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
vg0208432932 NA 1.97E-06 mr1741 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
vg0208432932 2.00E-06 2.00E-06 mr1996 Jap_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