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Detailed information for vg1215809668:

Variant ID: vg1215809668 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15809668
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.02, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

GCTCCAGTTATCTTTTTATTTTCCGCTGCATTTATGTAATACTTTTATAATGTTTGTAAGACGTGGATCTGTATGTCAAATTTGTCGTTTGTGTACCCCG[A/G]
CCGGTCCTGGACGGGGGTTTTAATGCACATTCTGCTTGGAATTCTATTCGGGAATTTCTGGGCGTGACACCTCATCTCAATCGGGCATTTAGTTATGGCC

Reverse complement sequence

GGCCATAACTAAATGCCCGATTGAGATGAGGTGTCACGCCCAGAAATTCCCGAATAGAATTCCAAGCAGAATGTGCATTAAAACCCCCGTCCAGGACCGG[T/C]
CGGGGTACACAAACGACAAATTTGACATACAGATCCACGTCTTACAAACATTATAAAAGTATTACATAAATGCAGCGGAAAATAAAAAGATAACTGGAGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.50%	36.20%	0.23%	0.00%	NA
All Indica	2759	43.60%	56.20%	0.22%	0.00%	NA
All Japonica	1512	96.20%	3.50%	0.26%	0.00%	NA
Aus	269	66.90%	33.10%	0.00%	0.00%	NA
Indica I	595	71.60%	28.40%	0.00%	0.00%	NA
Indica II	465	32.50%	67.50%	0.00%	0.00%	NA
Indica III	913	29.20%	70.40%	0.33%	0.00%	NA
Indica Intermediate	786	45.50%	54.10%	0.38%	0.00%	NA
Temperate Japonica	767	97.30%	2.50%	0.26%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	87.60%	11.60%	0.83%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	82.20%	16.70%	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
vg1215809668	A -> G	LOC_Os12g26980.1	downstream_gene_variant ; 4598.0bp to feature; MODIFIER	silent_mutation	Average:33.985; most accessible tissue: Minghui63 flag leaf, score: 57.188	N	N	N	N
vg1215809668	A -> G	LOC_Os12g26990.1	downstream_gene_variant ; 450.0bp to feature; MODIFIER	silent_mutation	Average:33.985; most accessible tissue: Minghui63 flag leaf, score: 57.188	N	N	N	N
vg1215809668	A -> G	LOC_Os12g27000.1	downstream_gene_variant ; 2442.0bp to feature; MODIFIER	silent_mutation	Average:33.985; most accessible tissue: Minghui63 flag leaf, score: 57.188	N	N	N	N
vg1215809668	A -> G	LOC_Os12g26980-LOC_Os12g26990	intergenic_region ; MODIFIER	silent_mutation	Average:33.985; most accessible tissue: Minghui63 flag leaf, score: 57.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215809668	4.69E-08	NA	mr1022	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
vg1215809668	1.65E-07	NA	mr1023	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
vg1215809668	1.00E-07	NA	mr1079	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
vg1215809668	2.55E-06	NA	mr1142	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
vg1215809668	3.44E-07	NA	mr1491	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
vg1215809668	NA	5.27E-10	mr1565	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
vg1215809668	NA	1.61E-08	mr1659	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
vg1215809668	3.05E-07	NA	mr1022_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