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Detailed information for vg0802736687:

Variant ID: vg0802736687 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2736687
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:

CCAAATTTGGTAACATCGGCATCGGAAAAGAAGATTAGATCAAAGTGGAATCGGAGGCGGAGATCAATTCGGGAACAGAGCAGGAATCGGCTAGAGTCCA[G/A]
ATCGGCTACGATTAGGATCGGCTGAGTATGAGTCGGACTAGGTAGGCTGATGCAGCCGATTCCGACAATACAACTTGGTGTGTGACATCGGGTTGAATTG

Reverse complement sequence

CAATTCAACCCGATGTCACACACCAAGTTGTATTGTCGGAATCGGCTGCATCAGCCTACCTAGTCCGACTCATACTCAGCCGATCCTAATCGTAGCCGAT[C/T]
TGGACTCTAGCCGATTCCTGCTCTGTTCCCGAATTGATCTCCGCCTCCGATTCCACTTTGATCTAATCTTCTTTTCCGATGCCGATGTTACCAAATTTGG

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	89.30%	7.80%	0.55%	2.39%	NA
All Indica	2759	81.70%	13.20%	0.94%	4.10%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	56.00%	39.00%	3.19%	1.85%	NA
Indica II	465	87.30%	12.30%	0.22%	0.22%	NA
Indica III	913	90.60%	0.00%	0.33%	9.09%	NA
Indica Intermediate	786	87.70%	9.70%	0.38%	2.29%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0802736687	G -> A	LOC_Os08g05250.1	intron_variant ; MODIFIER	silent_mutation	Average:45.44; most accessible tissue: Minghui63 young leaf, score: 65.92	N	N	N	N
vg0802736687	G -> DEL	N	N	silent_mutation	Average:45.44; most accessible tissue: Minghui63 young leaf, score: 65.92	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802736687	2.48E-06	2.48E-06	mr1027	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