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Detailed information for vg0826832590:

Variant ID: vg0826832590 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 26832590
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: 263. )

Flanking Sequence (100 bp) in Reference Genome:

AGAAACTTGGTTAAATTAAATACGGAGATATTGTGATTGGTTGAGAAGTAAAGATAGGTGGAAAAAAGTGAATTAATGGTGGATGGTTGTTATTGGATGG[G/A]
AAGAGAATTTTGGTGGAGAAATTGTTATATTTTAGTACAATTCCTAAGTTGTTAGTATATTTTGGCACCGAAGGAGGATAAGGATTTCGATCTAACTTGT

Reverse complement sequence

ACAAGTTAGATCGAAATCCTTATCCTCCTTCGGTGCCAAAATATACTAACAACTTAGGAATTGTACTAAAATATAACAATTTCTCCACCAAAATTCTCTT[C/T]
CCATCCAATAACAACCATCCACCATTAATTCACTTTTTTCCACCTATCTTTACTTCTCAACCAATCACAATATCTCCGTATTTAATTTAACCAAGTTTCT

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	97.60%	2.00%	0.38%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	92.60%	6.20%	1.19%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	80.20%	16.50%	3.37%	0.00%	NA
Japonica Intermediate	241	95.90%	4.10%	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
vg0826832590	G -> A	LOC_Os08g42460.1	downstream_gene_variant ; 2065.0bp to feature; MODIFIER	silent_mutation	Average:40.436; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0826832590	G -> A	LOC_Os08g42460-LOC_Os08g42470	intergenic_region ; MODIFIER	silent_mutation	Average:40.436; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0826832590	NA	4.16E-08	mr1622	Jap_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
vg0826832590	1.53E-06	1.31E-06	mr1794	Jap_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