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Detailed information for vg0708708061:

Variant ID: vg0708708061 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 8708061
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

TACATCTACGCACTCCCCTCTTTAAGAAACCGGTCTTTCTCCCTCTTCTCAAGAAAATCGGTCTCCTCCCTCCAATATAGTGTTACTGCATGTATATGAC[A/G]
TTACTGCACTTTTGACAGTAATATTGTGGTGAATTACAGTAAATCAGGAATTGAAACAAAAATATATAGGTTAAAGGTCTCAGATGTTACCCATATACTT

Reverse complement sequence

AAGTATATGGGTAACATCTGAGACCTTTAACCTATATATTTTTGTTTCAATTCCTGATTTACTGTAATTCACCACAATATTACTGTCAAAAGTGCAGTAA[T/C]
GTCATATACATGCAGTAACACTATATTGGAGGGAGGAGACCGATTTTCTTGAGAAGAGGGAGAAAGACCGGTTTCTTAAAGAGGGGAGTGCGTAGATGTA

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	87.90%	11.10%	0.95%	0.00%	NA
All Indica	2759	99.30%	0.70%	0.07%	0.00%	NA
All Japonica	1512	65.30%	32.10%	2.51%	0.00%	NA
Aus	269	95.90%	2.20%	1.86%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.10%	0.11%	0.00%	NA
Indica Intermediate	786	99.10%	0.80%	0.13%	0.00%	NA
Temperate Japonica	767	49.20%	47.30%	3.52%	0.00%	NA
Tropical Japonica	504	87.90%	11.10%	0.99%	0.00%	NA
Japonica Intermediate	241	69.70%	27.80%	2.49%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg0708708061	A -> G	LOC_Os07g15160.1	upstream_gene_variant ; 2061.0bp to feature; MODIFIER	silent_mutation	Average:33.391; most accessible tissue: Zhenshan97 young leaf, score: 60.8	N	N	N	N
vg0708708061	A -> G	LOC_Os07g15160.2	upstream_gene_variant ; 2061.0bp to feature; MODIFIER	silent_mutation	Average:33.391; most accessible tissue: Zhenshan97 young leaf, score: 60.8	N	N	N	N
vg0708708061	A -> G	LOC_Os07g15160-LOC_Os07g15170	intergenic_region ; MODIFIER	silent_mutation	Average:33.391; most accessible tissue: Zhenshan97 young leaf, score: 60.8	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0708708061	7.75E-06	NA	mr1400_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