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Detailed information for vg0802888568:

Variant ID: vg0802888568 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2888568
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.02, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTGGATCACCCTTGGATGAAAAACTTAAGGATTGGATGTTGGACATTTTACCTTTGATAGGCCTAAAAACTTCATGTATATATTATATCCAAACTAGA[G/T]
GTTATAAGTGTGTTTTGGCTATGTGCATCATAGCTATGCAAATGCCGGGAGTATGCTCAACATAGTTGTATCGCCTCATTGTAATTGACTGCGTTCAATA

Reverse complement sequence

TATTGAACGCAGTCAATTACAATGAGGCGATACAACTATGTTGAGCATACTCCCGGCATTTGCATAGCTATGATGCACATAGCCAAAACACACTTATAAC[C/A]
TCTAGTTTGGATATAATATATACATGAAGTTTTTAGGCCTATCAAAGGTAAAATGTCCAACATCCAATCCTTAAGTTTTTCATCCAAGGGTGATCCAAGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.70%	38.80%	0.47%	0.00%	NA
All Indica	2759	49.50%	49.80%	0.65%	0.00%	NA
All Japonica	1512	77.50%	22.40%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	49.60%	50.30%	0.17%	0.00%	NA
Indica II	465	32.90%	66.00%	1.08%	0.00%	NA
Indica III	913	57.90%	41.70%	0.33%	0.00%	NA
Indica Intermediate	786	49.60%	49.20%	1.15%	0.00%	NA
Temperate Japonica	767	85.10%	14.70%	0.13%	0.00%	NA
Tropical Japonica	504	80.40%	19.60%	0.00%	0.00%	NA
Japonica Intermediate	241	47.30%	52.70%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	88.50%	2.08%	0.00%	NA
Intermediate	90	60.00%	38.90%	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
vg0802888568	G -> T	LOC_Os08g05440.1	intron_variant ; MODIFIER	silent_mutation	Average:62.485; most accessible tissue: Callus, score: 83.676	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802888568	3.29E-06	7.36E-06	mr1566_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