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Detailed information for vg0827210810:

Variant ID: vg0827210810 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 27210810
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

TCGACTTCAACCCTTTTAAACCTTAAACCAAAACATAGCTTCACATGATTTGCTCACTGCCCTTCAAACCAACTGGACCTGCAATGAGAGAAAAAAAATT[G/A]
AAGCATGTGATGCTGAGTTCCATATACAAACAACGTGTGTCAGATAATACTCTACATATAGCCTGATAAAAGAAACTAGACGCCGATGTAAAATGTATAT

Reverse complement sequence

ATATACATTTTACATCGGCGTCTAGTTTCTTTTATCAGGCTATATGTAGAGTATTATCTGACACACGTTGTTTGTATATGGAACTCAGCATCACATGCTT[C/T]
AATTTTTTTTCTCTCATTGCAGGTCCAGTTGGTTTGAAGGGCAGTGAGCAAATCATGTGAAGCTATGTTTTGGTTTAAGGTTTAAAAGGGTTGAAGTCGA

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	95.30%	4.60%	0.04%	0.00%	NA
All Indica	2759	92.20%	7.70%	0.07%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	98.00%	2.00%	0.00%	0.00%	NA
Indica II	465	98.70%	0.90%	0.43%	0.00%	NA
Indica III	913	84.00%	16.00%	0.00%	0.00%	NA
Indica Intermediate	786	93.50%	6.50%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0827210810	G -> A	LOC_Os08g43050.1	upstream_gene_variant ; 859.0bp to feature; MODIFIER	silent_mutation	Average:76.439; most accessible tissue: Callus, score: 91.458	N	N	N	N
vg0827210810	G -> A	LOC_Os08g43060.1	intron_variant ; MODIFIER	silent_mutation	Average:76.439; most accessible tissue: Callus, score: 91.458	N	N	N	N
vg0827210810	G -> A	LOC_Os08g43060.2	intron_variant ; MODIFIER	silent_mutation	Average:76.439; most accessible tissue: Callus, score: 91.458	N	N	N	N
vg0827210810	G -> A	LOC_Os08g43060.3	intron_variant ; MODIFIER	silent_mutation	Average:76.439; most accessible tissue: Callus, score: 91.458	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0827210810	NA	2.88E-08	mr1078	Ind_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
vg0827210810	NA	1.64E-06	mr1094	Ind_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
vg0827210810	NA	1.21E-06	mr1096	Ind_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
vg0827210810	NA	1.08E-06	mr1121	Ind_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
vg0827210810	3.35E-08	7.16E-08	mr1246	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
vg0827210810	NA	2.70E-06	mr1731	Ind_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
vg0827210810	NA	2.59E-06	mr1768	Ind_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
vg0827210810	NA	5.30E-07	mr1973	Ind_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