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Detailed information for vg0825569796:

Variant ID: vg0825569796 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25569796
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

CCACAACAGCGGCAGCAGCAAGCGCGCCGATGACCCGAAGCCGAGGCTCGAGGCGAGGATGACGACGATGAGAAGGCAGCGGCGGTGGTGGCATGCCACC[G/A]
ACTCCCTCTAGCTTGGACCACCTAGGTACAGCTGCAGATGAGCAGGGACGAGGAGCAGGCCCGCCATCAAACAGAGCGGCGGTGTCACGCCCTGAAGTTC

Reverse complement sequence

GAACTTCAGGGCGTGACACCGCCGCTCTGTTTGATGGCGGGCCTGCTCCTCGTCCCTGCTCATCTGCAGCTGTACCTAGGTGGTCCAAGCTAGAGGGAGT[C/T]
GGTGGCATGCCACCACCGCCGCTGCCTTCTCATCGTCGTCATCCTCGCCTCGAGCCTCGGCTTCGGGTCATCGGCGCGCTTGCTGCTGCCGCTGTTGTGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.90%	9.60%	1.59%	16.89%	NA
All Indica	2759	56.60%	14.10%	1.85%	27.44%	NA
All Japonica	1512	97.10%	0.70%	0.53%	1.72%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	27.20%	31.30%	3.53%	37.98%	NA
Indica II	465	38.30%	6.50%	2.15%	53.12%	NA
Indica III	913	88.40%	8.00%	0.22%	3.40%	NA
Indica Intermediate	786	52.70%	12.80%	2.29%	32.19%	NA
Temperate Japonica	767	97.30%	0.80%	0.65%	1.30%	NA
Tropical Japonica	504	98.80%	0.00%	0.40%	0.79%	NA
Japonica Intermediate	241	92.90%	1.70%	0.41%	4.98%	NA
VI/Aromatic	96	31.20%	54.20%	14.58%	0.00%	NA
Intermediate	90	76.70%	4.40%	2.22%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0825569796	G -> A	LOC_Os08g40380.1	upstream_gene_variant ; 4355.0bp to feature; MODIFIER	silent_mutation	Average:30.522; most accessible tissue: Zhenshan97 root, score: 68.908	N	N	N	N
vg0825569796	G -> A	LOC_Os08g40390.1	upstream_gene_variant ; 1978.0bp to feature; MODIFIER	silent_mutation	Average:30.522; most accessible tissue: Zhenshan97 root, score: 68.908	N	N	N	N
vg0825569796	G -> A	LOC_Os08g40390-LOC_Os08g40410	intergenic_region ; MODIFIER	silent_mutation	Average:30.522; most accessible tissue: Zhenshan97 root, score: 68.908	N	N	N	N
vg0825569796	G -> DEL	N	N	silent_mutation	Average:30.522; most accessible tissue: Zhenshan97 root, score: 68.908	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825569796	1.44E-12	3.74E-18	mr1874	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
vg0825569796	1.78E-13	2.29E-17	mr1874	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
vg0825569796	NA	2.11E-08	mr1709_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
vg0825569796	7.69E-09	NA	mr1874_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
vg0825569796	4.11E-10	6.29E-15	mr1874_2	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