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Detailed information for vg0801689793:

Variant ID: vg0801689793 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1689793
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

TCACAAAAATAAATATTAATAGCAAATTTATCACAAAACTAAATGTTTTAGTGCCAATTTAATCATAAAACTGCAACGTTTATAGCTCCAACATAACCGC[G/A]
GTGCTAGGGATTTAAACTCTATAATCTGTAGTTTTGTGATAATTTCAATATTAAATATGTAATTTTGTGATACTTGGCCTTAATTAAATTTGTAATTTTG

Reverse complement sequence

CAAAATTACAAATTTAATTAAGGCCAAGTATCACAAAATTACATATTTAATATTGAAATTATCACAAAACTACAGATTATAGAGTTTAAATCCCTAGCAC[C/T]
GCGGTTATGTTGGAGCTATAAACGTTGCAGTTTTATGATTAAATTGGCACTAAAACATTTAGTTTTGTGATAAATTTGCTATTAATATTTATTTTTGTGA

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	63.60%	36.30%	0.11%	0.00%	NA
All Indica	2759	42.20%	57.60%	0.18%	0.00%	NA
All Japonica	1512	97.90%	2.10%	0.00%	0.00%	NA
Aus	269	76.60%	23.40%	0.00%	0.00%	NA
Indica I	595	33.10%	66.40%	0.50%	0.00%	NA
Indica II	465	10.30%	89.50%	0.22%	0.00%	NA
Indica III	913	72.20%	27.70%	0.11%	0.00%	NA
Indica Intermediate	786	33.20%	66.80%	0.00%	0.00%	NA
Temperate Japonica	767	97.00%	3.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	68.90%	31.10%	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
vg0801689793	G -> A	LOC_Os08g03610.1	upstream_gene_variant ; 989.0bp to feature; MODIFIER	silent_mutation	Average:25.792; most accessible tissue: Callus, score: 48.325	N	N	N	N
vg0801689793	G -> A	LOC_Os08g03610-LOC_Os08g03620	intergenic_region ; MODIFIER	silent_mutation	Average:25.792; most accessible tissue: Callus, score: 48.325	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801689793	NA	7.19E-07	mr1709	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
vg0801689793	NA	7.09E-11	mr1739	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
vg0801689793	NA	1.34E-07	mr1817	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
vg0801689793	NA	8.84E-12	mr1739_2	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