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Detailed information for vg0207732987:

Variant ID: vg0207732987 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7732987
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, A: 0.02, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

AACCAATCGTGGAAATGATATATCCTACTAGCAAAGGACACGTGGATCATCCAAAACGATCCAACTTATTCCATCGAAGTGCTCAAACTTCTCCATTACC[G/A]
TCACCAAACTCACCTCCAAAGCCACTACTACCATCAAATCCACCATTGAGGGCAGCCACCTTTGAAGCTGCAATTTGTGTCCTCATAGCCAACACATATG

Reverse complement sequence

CATATGTGTTGGCTATGAGGACACAAATTGCAGCTTCAAAGGTGGCTGCCCTCAATGGTGGATTTGATGGTAGTAGTGGCTTTGGAGGTGAGTTTGGTGA[C/T]
GGTAATGGAGAAGTTTGAGCACTTCGATGGAATAAGTTGGATCGTTTTGGATGATCCACGTGTCCTTTGCTAGTAGGATATATCATTTCCACGATTGGTT

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	87.30%	12.00%	0.68%	0.00%	NA
All Indica	2759	89.60%	9.30%	1.12%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	14.90%	85.10%	0.00%	0.00%	NA
Indica I	595	79.70%	17.50%	2.86%	0.00%	NA
Indica II	465	94.60%	4.90%	0.43%	0.00%	NA
Indica III	913	95.40%	4.60%	0.00%	0.00%	NA
Indica Intermediate	786	87.30%	11.20%	1.53%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	41.70%	58.30%	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
vg0207732987	G -> A	LOC_Os02g14140.1	downstream_gene_variant ; 285.0bp to feature; MODIFIER	silent_mutation	Average:19.274; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0207732987	G -> A	LOC_Os02g14130-LOC_Os02g14140	intergenic_region ; MODIFIER	silent_mutation	Average:19.274; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207732987	1.84E-10	1.97E-16	mr1570	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
vg0207732987	3.20E-07	1.00E-06	mr1570	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
vg0207732987	4.89E-08	1.11E-07	mr1570_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