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Detailed information for vg0825021665:

Variant ID: vg0825021665 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25021665
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, A: 0.23, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTAAACTACTAAACGGCGTGTTTTTATGCAACTATATATATATACCCACACACACGACAGTTGTTTTGAAAAAATTATATTAATCCATTTTGCAAAAA[T/A]
AATAATACTTAATTATTTATGTAAGAATATGTGCTTCGTTTTACGTGCCAGGAACCCCTTCCGAACGCAGCCTAAAAGTTTTACTCGTAATTTATCTTTG

Reverse complement sequence

CAAAGATAAATTACGAGTAAAACTTTTAGGCTGCGTTCGGAAGGGGTTCCTGGCACGTAAAACGAAGCACATATTCTTACATAAATAATTAAGTATTATT[A/T]
TTTTTGCAAAATGGATTAATATAATTTTTTCAAAACAACTGTCGTGTGTGTGGGTATATATATATAGTTGCATAAAAACACGCCGTTTAGTAGTTTAAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.50%	31.30%	0.19%	0.00%	NA
All Indica	2759	56.30%	43.50%	0.18%	0.00%	NA
All Japonica	1512	99.50%	0.40%	0.07%	0.00%	NA
Aus	269	6.30%	93.70%	0.00%	0.00%	NA
Indica I	595	65.70%	33.90%	0.34%	0.00%	NA
Indica II	465	69.70%	29.90%	0.43%	0.00%	NA
Indica III	913	39.80%	60.20%	0.00%	0.00%	NA
Indica Intermediate	786	60.60%	39.30%	0.13%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	77.80%	18.90%	3.33%	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
vg0825021665	T -> A	LOC_Os08g39550.1	upstream_gene_variant ; 4302.0bp to feature; MODIFIER	silent_mutation	Average:47.639; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0825021665	T -> A	LOC_Os08g39560.1	upstream_gene_variant ; 1650.0bp to feature; MODIFIER	silent_mutation	Average:47.639; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0825021665	T -> A	LOC_Os08g39550-LOC_Os08g39560	intergenic_region ; MODIFIER	silent_mutation	Average:47.639; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825021665	NA	5.99E-06	mr1699	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
vg0825021665	9.55E-18	1.08E-40	mr1874	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
vg0825021665	1.66E-16	1.85E-22	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
vg0825021665	NA	2.76E-08	mr1004_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
vg0825021665	NA	2.28E-10	mr1193_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
vg0825021665	3.26E-09	NA	mr1699_2	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
vg0825021665	1.43E-08	1.39E-12	mr1699_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
vg0825021665	2.82E-20	9.07E-57	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
vg0825021665	6.45E-19	1.09E-27	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