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Detailed information for vg0809346327:

Variant ID: vg0809346327 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9346327
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.88, G: 0.12, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

TTCAAATGTGTGTCCGTATATCTGATGTGACACGGCAAAAATTTTCACCCTTGGATCTAAACACACTTAGTTAAACTTGAAGTAGTTTGACTTTGACCAA[A/G]
ATCAAAATGACTTATAATCTGAAATAGAGGGAGTAATTACCGCAGCATCTTCACTTCTCTAACAAGTTCTACCTCTTTTAATAAAAGACCTTATTTTCAG

Reverse complement sequence

CTGAAAATAAGGTCTTTTATTAAAAGAGGTAGAACTTGTTAGAGAAGTGAAGATGCTGCGGTAATTACTCCCTCTATTTCAGATTATAAGTCATTTTGAT[T/C]
TTGGTCAAAGTCAAACTACTTCAAGTTTAACTAAGTGTGTTTAGATCCAAGGGTGAAAATTTTTGCCGTGTCACATCAGATATACGGACACACATTTGAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.50%	26.40%	0.06%	0.02%	NA
All Indica	2759	63.40%	36.50%	0.07%	0.00%	NA
All Japonica	1512	93.70%	6.30%	0.00%	0.00%	NA
Aus	269	56.10%	43.90%	0.00%	0.00%	NA
Indica I	595	65.00%	34.80%	0.17%	0.00%	NA
Indica II	465	88.60%	11.40%	0.00%	0.00%	NA
Indica III	913	44.20%	55.60%	0.11%	0.00%	NA
Indica Intermediate	786	69.50%	30.50%	0.00%	0.00%	NA
Temperate Japonica	767	98.20%	1.80%	0.00%	0.00%	NA
Tropical Japonica	504	87.30%	12.70%	0.00%	0.00%	NA
Japonica Intermediate	241	92.50%	7.50%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	7.30%	1.04%	0.00%	NA
Intermediate	90	77.80%	21.10%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0809346327	A -> G	LOC_Os08g15340.1	upstream_gene_variant ; 2788.0bp to feature; MODIFIER	silent_mutation	Average:32.362; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0809346327	A -> G	LOC_Os08g15340-LOC_Os08g15350	intergenic_region ; MODIFIER	silent_mutation	Average:32.362; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0809346327	A -> DEL	N	N	silent_mutation	Average:32.362; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809346327	NA	3.25E-06	mr1919	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