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Detailed information for vg1213470463:

Variant ID: vg1213470463 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13470463
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.87, A: 0.14, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

TAGATATTAACAATATATAATTCTTATATCGATATATACTTAAATCAAGTGATTGGGATAGATCGGTCGCCATGCCGAGACAGTATAAATCACTTAGATC[A/G]
AAATATATATTAATAAAGCATAGCCGATCAGATAGATCTAGCATGTATTGGCTAATACTCCGATACTACTCTATGTTAAGATGTTAAAACAAGCAGAATA

Reverse complement sequence

TATTCTGCTTGTTTTAACATCTTAACATAGAGTAGTATCGGAGTATTAGCCAATACATGCTAGATCTATCTGATCGGCTATGCTTTATTAATATATATTT[T/C]
GATCTAAGTGATTTATACTGTCTCGGCATGGCGACCGATCTATCCCAATCACTTGATTTAAGTATATATCGATATAAGAATTATATATTGTTAATATCTA

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	77.40%	17.50%	5.12%	0.00%	NA
All Indica	2759	88.70%	4.20%	7.07%	0.00%	NA
All Japonica	1512	52.90%	44.60%	2.45%	0.00%	NA
Aus	269	95.50%	2.20%	2.23%	0.00%	NA
Indica I	595	90.90%	1.50%	7.56%	0.00%	NA
Indica II	465	89.00%	4.90%	6.02%	0.00%	NA
Indica III	913	86.20%	5.30%	8.54%	0.00%	NA
Indica Intermediate	786	89.70%	4.70%	5.60%	0.00%	NA
Temperate Japonica	767	21.60%	77.70%	0.65%	0.00%	NA
Tropical Japonica	504	90.70%	4.40%	4.96%	0.00%	NA
Japonica Intermediate	241	73.40%	23.70%	2.90%	0.00%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	67.80%	28.90%	3.33%	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
vg1213470463	A -> G	LOC_Os12g23730.1	upstream_gene_variant ; 3152.0bp to feature; MODIFIER	silent_mutation	Average:31.643; most accessible tissue: Minghui63 root, score: 40.262	N	N	N	N
vg1213470463	A -> G	LOC_Os12g23730-LOC_Os12g23750	intergenic_region ; MODIFIER	silent_mutation	Average:31.643; most accessible tissue: Minghui63 root, score: 40.262	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213470463	6.34E-07	NA	mr1454	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
vg1213470463	3.70E-06	3.70E-06	mr1516	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
vg1213470463	6.83E-06	NA	mr1844	Jap_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
vg1213470463	NA	9.86E-06	mr1492_2	Jap_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