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Detailed information for vg0817258360:

Variant ID: vg0817258360 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17258360
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:

AGAACGAATAGTAATAACTCGTACACTTTTCGTGGTGTATATTAGTGTGTAACCAAGAAGTTTGGTTGTATAAATCCATTCTTTCCATGTCACAAGACAA[G/A]
TTTATTCACTATATGCGATTATATTTTGGAAAAATATATATGATCAAATAAGCACATTATGCATATATAATTTTGACTTGACATAGTCCACCCTTTCGTG

Reverse complement sequence

CACGAAAGGGTGGACTATGTCAAGTCAAAATTATATATGCATAATGTGCTTATTTGATCATATATATTTTTCCAAAATATAATCGCATATAGTGAATAAA[C/T]
TTGTCTTGTGACATGGAAAGAATGGATTTATACAACCAAACTTCTTGGTTACACACTAATATACACCACGAAAAGTGTACGAGTTATTACTATTCGTTCT

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	61.80%	31.80%	0.63%	5.76%	NA
All Indica	2759	89.30%	3.40%	0.07%	7.21%	NA
All Japonica	1512	9.10%	84.50%	1.85%	4.56%	NA
Aus	269	98.50%	1.10%	0.00%	0.37%	NA
Indica I	595	92.90%	5.00%	0.17%	1.85%	NA
Indica II	465	95.90%	3.20%	0.00%	0.86%	NA
Indica III	913	84.80%	1.10%	0.11%	14.02%	NA
Indica Intermediate	786	87.80%	5.10%	0.00%	7.12%	NA
Temperate Japonica	767	2.00%	94.80%	3.26%	0.00%	NA
Tropical Japonica	504	21.00%	65.30%	0.60%	13.10%	NA
Japonica Intermediate	241	6.60%	92.10%	0.00%	1.24%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	52.20%	44.40%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817258360	G -> A	LOC_Os08g28270.1	upstream_gene_variant ; 269.0bp to feature; MODIFIER	silent_mutation	Average:47.227; most accessible tissue: Minghui63 root, score: 89.417	N	N	N	N
vg0817258360	G -> A	LOC_Os08g28270-LOC_Os08g28280	intergenic_region ; MODIFIER	silent_mutation	Average:47.227; most accessible tissue: Minghui63 root, score: 89.417	N	N	N	N
vg0817258360	G -> DEL	N	N	silent_mutation	Average:47.227; most accessible tissue: Minghui63 root, score: 89.417	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817258360	NA	4.49E-12	mr1198	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
vg0817258360	NA	4.17E-06	mr1681	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
vg0817258360	NA	4.47E-11	mr1537_2	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
vg0817258360	NA	7.11E-08	mr1783_2	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
vg0817258360	NA	1.16E-07	mr1804_2	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
vg0817258360	NA	6.27E-09	mr1947_2	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