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Detailed information for vg1203618566:

Variant ID: vg1203618566 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 3618566
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

CAGTCCCGTGCTTGTTTTTCATTTTTCATTGTAAATAACTTTTATTTCTCTTAATGAAAAAAAATGCGCTCCTTGCGTATTCCTAAAAAAACAATATTCA[G/A]
AAATTGTTCGACAGGCAGGTACAGCATTTCGTGGTTCAGAAATTCAGAGAAATGGGCTATACCGTTTTGGCGCCAGAAGCTTTCCTGTCATGTTTCATAG

Reverse complement sequence

CTATGAAACATGACAGGAAAGCTTCTGGCGCCAAAACGGTATAGCCCATTTCTCTGAATTTCTGAACCACGAAATGCTGTACCTGCCTGTCGAACAATTT[C/T]
TGAATATTGTTTTTTTAGGAATACGCAAGGAGCGCATTTTTTTTCATTAAGAGAAATAAAAGTTATTTACAATGAAAAATGAAAAACAAGCACGGGACTG

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	80.80%	19.00%	0.21%	0.00%	NA
All Indica	2759	97.40%	2.50%	0.11%	0.00%	NA
All Japonica	1512	52.80%	46.80%	0.40%	0.00%	NA
Aus	269	97.00%	3.00%	0.00%	0.00%	NA
Indica I	595	98.70%	1.20%	0.17%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	95.70%	4.20%	0.11%	0.00%	NA
Indica Intermediate	786	97.20%	2.70%	0.13%	0.00%	NA
Temperate Japonica	767	58.10%	41.50%	0.39%	0.00%	NA
Tropical Japonica	504	52.80%	46.80%	0.40%	0.00%	NA
Japonica Intermediate	241	35.70%	63.90%	0.41%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	66.70%	32.20%	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
vg1203618566	G -> A	LOC_Os12g07350.1	upstream_gene_variant ; 785.0bp to feature; MODIFIER	silent_mutation	Average:70.879; most accessible tissue: Zhenshan97 flag leaf, score: 89.689	N	N	N	N
vg1203618566	G -> A	LOC_Os12g07340-LOC_Os12g07350	intergenic_region ; MODIFIER	silent_mutation	Average:70.879; most accessible tissue: Zhenshan97 flag leaf, score: 89.689	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1203618566	NA	6.53E-06	mr1940	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
vg1203618566	8.19E-06	NA	mr1019_2	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
vg1203618566	6.40E-07	NA	mr1164_2	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
vg1203618566	NA	6.05E-08	mr1164_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
vg1203618566	NA	3.87E-06	mr1561_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
vg1203618566	8.71E-06	NA	mr1648_2	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
vg1203618566	NA	2.79E-10	mr1947_2	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