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Detailed information for vg1215036442:

Variant ID: vg1215036442 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15036442
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: 0.02, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CTCGAACTATATCACTCTCTCTCCCTCTCTCTTCCCCAGTATAAACCATGCTACCACTGCCAAATATACATACTCCTTCCTTCCCTAAATGTTTGACGCC[G/A]
TTGACTTTTTAAACATGTTTAATCGTTCGTCTTATTCAAAAACTTTTGTGAAATATATAAAACTATATATATACATTAAAGTATATTTAACAATGAATCA

Reverse complement sequence

TGATTCATTGTTAAATATACTTTAATGTATATATATAGTTTTATATATTTCACAAAAGTTTTTGAATAAGACGAACGATTAAACATGTTTAAAAAGTCAA[C/T]
GGCGTCAAACATTTAGGGAAGGAAGGAGTATGTATATTTGGCAGTGGTAGCATGGTTTATACTGGGGAAGAGAGAGGGAGAGAGAGTGATATAGTTCGAG

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	66.40%	33.50%	0.15%	0.00%	NA
All Indica	2759	53.50%	46.20%	0.22%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	27.10%	72.90%	0.00%	0.00%	NA
Indica I	595	56.80%	42.70%	0.50%	0.00%	NA
Indica II	465	64.70%	35.30%	0.00%	0.00%	NA
Indica III	913	44.20%	55.50%	0.22%	0.00%	NA
Indica Intermediate	786	55.20%	44.70%	0.13%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	20.80%	79.20%	0.00%	0.00%	NA
Intermediate	90	73.30%	25.60%	1.11%	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
vg1215036442	G -> A	LOC_Os12g25920.1	upstream_gene_variant ; 2471.0bp to feature; MODIFIER	silent_mutation	Average:61.238; most accessible tissue: Zhenshan97 young leaf, score: 78.044	N	N	N	N
vg1215036442	G -> A	LOC_Os12g25910-LOC_Os12g25920	intergenic_region ; MODIFIER	silent_mutation	Average:61.238; most accessible tissue: Zhenshan97 young leaf, score: 78.044	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215036442	NA	2.91E-07	mr1002	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
vg1215036442	NA	3.37E-11	mr1002_2	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