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Detailed information for vg0809300703:

Variant ID: vg0809300703 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9300703
Reference Allele: G	Alternative Allele: A
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: 116. )

Flanking Sequence (100 bp) in Reference Genome:

AAATTGAACTGATAAAAATCACACTCCATTATTATTATAGTAGCCCCCGACTGGTAACTCAAGAGATGACTTGATGTTGGCAGTCAAAGAGGGAAAGAAT[G/A]
TACAAAAGTAATGCCTAAGCATAAAAACGACGAAGATGCTCAATATTCCAATAGTTGTCGACGTGACTACCGTCTTCGCGCTTTAGTCGATAAGAACCTG

Reverse complement sequence

CAGGTTCTTATCGACTAAAGCGCGAAGACGGTAGTCACGTCGACAACTATTGGAATATTGAGCATCTTCGTCGTTTTTATGCTTAGGCATTACTTTTGTA[C/T]
ATTCTTTCCCTCTTTGACTGCCAACATCAAGTCATCTCTTGAGTTACCAGTCGGGGGCTACTATAATAATAATGGAGTGTGATTTTTATCAGTTCAATTT

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	73.70%	19.60%	2.56%	4.13%	NA
All Indica	2759	58.90%	31.10%	4.17%	5.87%	NA
All Japonica	1512	99.40%	0.40%	0.07%	0.13%	NA
Aus	269	67.70%	19.70%	1.86%	10.78%	NA
Indica I	595	60.50%	28.10%	5.38%	6.05%	NA
Indica II	465	74.00%	7.10%	4.30%	14.62%	NA
Indica III	913	48.40%	47.50%	2.74%	1.31%	NA
Indica Intermediate	786	60.80%	28.50%	4.83%	5.85%	NA
Temperate Japonica	767	99.60%	0.10%	0.13%	0.13%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	87.80%	10.00%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0809300703	G -> A	LOC_Os08g15300.1	downstream_gene_variant ; 1275.0bp to feature; MODIFIER	silent_mutation	Average:44.054; most accessible tissue: Zhenshan97 young leaf, score: 65.804	N	N	N	N
vg0809300703	G -> A	LOC_Os08g15290.1	intron_variant ; MODIFIER	silent_mutation	Average:44.054; most accessible tissue: Zhenshan97 young leaf, score: 65.804	N	N	N	N
vg0809300703	G -> DEL	N	N	silent_mutation	Average:44.054; most accessible tissue: Zhenshan97 young leaf, score: 65.804	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809300703	2.47E-06	NA	mr1005	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