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Detailed information for vg0825053682:

Variant ID: vg0825053682 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25053682
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTTAAGGCCTCCTCAAATGTTACTATATAGGCACTAAAATACAAAGCATGAAAAATGAAAAACCACAAAAAGCATGTTAAAGTGGACTTGGGAAAAAA[A/T]
TACCTGTGCCATATTGGTAGAAATTGTTACGATGTATGTCACTTTGTAGAACTCTCTCCATACCATCTGTTTTTGTGACCTAGGTGGTTATCTGCCTTCA

Reverse complement sequence

TGAAGGCAGATAACCACCTAGGTCACAAAAACAGATGGTATGGAGAGAGTTCTACAAAGTGACATACATCGTAACAATTTCTACCAATATGGCACAGGTA[T/A]
TTTTTTCCCAAGTCCACTTTAACATGCTTTTTGTGGTTTTTCATTTTTCATGCTTTGTATTTTAGTGCCTATATAGTAACATTTGAGGAGGCCTTAAAGG

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	82.40%	16.80%	0.89%	0.00%	NA
All Indica	2759	96.80%	2.50%	0.65%	0.00%	NA
All Japonica	1512	51.90%	46.60%	1.46%	0.00%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	91.60%	7.10%	1.34%	0.00%	NA
Indica II	465	97.80%	1.50%	0.65%	0.00%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	96.70%	2.50%	0.76%	0.00%	NA
Temperate Japonica	767	33.90%	64.40%	1.69%	0.00%	NA
Tropical Japonica	504	69.80%	29.40%	0.79%	0.00%	NA
Japonica Intermediate	241	71.80%	26.10%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	80.00%	18.90%	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
vg0825053682	A -> T	LOC_Os08g39580-LOC_Os08g39590	intergenic_region ; MODIFIER	silent_mutation	Average:70.495; most accessible tissue: Callus, score: 88.487	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825053682	NA	5.11E-11	mr1712	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
vg0825053682	NA	4.16E-08	mr1576_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
vg0825053682	3.32E-06	9.80E-07	mr1786_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
vg0825053682	4.51E-06	NA	mr1786_2	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