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Detailed information for vg0803221452:

Variant ID: vg0803221452 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 3221452
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

AAAACGAAGAGTAGGGGGGACTGAAGAAGGAAGAAGGAAATGAGTCCCCCCTTAAATCTTATTCTGGATCTGCCCATGTGTACAACCGTGTGTAATAGTG[G/A]
TCTCTCTTTGTTGCCATGTAAGTAAATTTGATGATGTGGAAGAAAGAGGAGAGGAAAGATAAAGCATGGTTGCTATGTATGACAACAGCTCAGAGTCGAC

Reverse complement sequence

GTCGACTCTGAGCTGTTGTCATACATAGCAACCATGCTTTATCTTTCCTCTCCTCTTTCTTCCACATCATCAAATTTACTTACATGGCAACAAAGAGAGA[C/T]
CACTATTACACACGGTTGTACACATGGGCAGATCCAGAATAAGATTTAAGGGGGGACTCATTTCCTTCTTCCTTCTTCAGTCCCCCCTACTCTTCGTTTT

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	79.10%	18.00%	2.84%	0.00%	NA
All Indica	2759	66.00%	29.70%	4.28%	0.00%	NA
All Japonica	1512	98.70%	0.50%	0.73%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	62.20%	29.40%	8.40%	0.00%	NA
Indica II	465	76.80%	20.40%	2.80%	0.00%	NA
Indica III	913	66.00%	32.90%	1.10%	0.00%	NA
Indica Intermediate	786	62.60%	31.70%	5.73%	0.00%	NA
Temperate Japonica	767	98.80%	0.00%	1.17%	0.00%	NA
Tropical Japonica	504	98.60%	1.00%	0.40%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	70.00%	24.40%	5.56%	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
vg0803221452	G -> A	LOC_Os08g05940.1	downstream_gene_variant ; 2774.0bp to feature; MODIFIER	silent_mutation	Average:68.353; most accessible tissue: Callus, score: 81.187	N	N	N	N
vg0803221452	G -> A	LOC_Os08g05930-LOC_Os08g05940	intergenic_region ; MODIFIER	silent_mutation	Average:68.353; most accessible tissue: Callus, score: 81.187	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0803221452	1.66E-06	5.33E-06	mr1892	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