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Detailed information for vg0208312505:

Variant ID: vg0208312505 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8312505
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

GAAGTTTGGGGAACAGAAATCTAGTGGTAATCCTCATGCTCAAGACATTATCGATCTAATGACAAGGTATAATTTGAGAAATAGAAACCTGCAAATTAAT[G/A]
ATTTATCACCTGAATAATGCTGATAATTGCCACTTCTGATGTGCCCAATAAAGGTATCCAGCTCTACGTGTCGCCTACATTGAAGAGAAGGAGATCATAG

Reverse complement sequence

CTATGATCTCCTTCTCTTCAATGTAGGCGACACGTAGAGCTGGATACCTTTATTGGGCACATCAGAAGTGGCAATTATCAGCATTATTCAGGTGATAAAT[C/T]
ATTAATTTGCAGGTTTCTATTTCTCAAATTATACCTTGTCATTAGATCGATAATGTCTTGAGCATGAGGATTACCACTAGATTTCTGTTCCCCAAACTTC

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	91.60%	8.40%	0.00%	0.00%	NA
All Indica	2759	86.20%	13.80%	0.00%	0.00%	NA
All Japonica	1512	99.40%	0.60%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.00%	5.00%	0.00%	0.00%	NA
Indica II	465	66.00%	34.00%	0.00%	0.00%	NA
Indica III	913	89.70%	10.30%	0.00%	0.00%	NA
Indica Intermediate	786	87.30%	12.70%	0.00%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0208312505	G -> A	LOC_Os02g14900.1	intron_variant ; MODIFIER	silent_mutation	Average:38.179; most accessible tissue: Callus, score: 68.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208312505	NA	5.67E-06	mr1293	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
vg0208312505	1.25E-06	7.58E-08	mr1392	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
vg0208312505	8.32E-06	3.36E-06	mr1507	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
vg0208312505	NA	9.38E-06	mr1838	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