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Detailed information for vg1215481439:

Variant ID: vg1215481439 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15481439
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

GCCGAGCCGGCCCAAGAGGGGGAGCGGGGGAATTTTAAGGTTTTTCTTTTTATAAAATCATTTTAACTTTGTTTATTTCTTAATAATTATTATTTGTGCT[C/A]
TGAAAATTCCACTAAAATTTATTTACACATTTTAGGCTTTTAGGAAATATACAAAAATCCTCCAAGCCTTATTTGACTTTTAACTTTGCACATTTTAATT

Reverse complement sequence

AATTAAAATGTGCAAAGTTAAAAGTCAAATAAGGCTTGGAGGATTTTTGTATATTTCCTAAAAGCCTAAAATGTGTAAATAAATTTTAGTGGAATTTTCA[G/T]
AGCACAAATAATAATTATTAAGAAATAAACAAAGTTAAAATGATTTTATAAAAAGAAAAACCTTAAAATTCCCCCGCTCCCCCTCTTGGGCCGGCTCGGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.90%	8.90%	0.47%	13.71%	NA
All Indica	2759	79.80%	14.90%	0.43%	4.86%	NA
All Japonica	1512	74.70%	0.40%	0.26%	24.67%	NA
Aus	269	67.70%	0.00%	1.49%	30.86%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	37.00%	44.10%	0.86%	18.06%	NA
Indica III	913	89.80%	8.20%	0.33%	1.64%	NA
Indica Intermediate	786	78.80%	16.20%	0.64%	4.45%	NA
Temperate Japonica	767	96.70%	0.70%	0.00%	2.61%	NA
Tropical Japonica	504	38.50%	0.00%	0.79%	60.71%	NA
Japonica Intermediate	241	80.10%	0.40%	0.00%	19.50%	NA
VI/Aromatic	96	49.00%	0.00%	2.08%	48.96%	NA
Intermediate	90	83.30%	4.40%	0.00%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215481439	C -> DEL	N	N	silent_mutation	Average:25.904; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg1215481439	C -> A	LOC_Os12g26480-LOC_Os12g26500	intergenic_region ; MODIFIER	silent_mutation	Average:25.904; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215481439	NA	1.33E-07	mr1024_2	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
vg1215481439	NA	1.21E-10	mr1565_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
vg1215481439	1.24E-06	NA	mr1584_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
vg1215481439	9.61E-08	9.61E-08	mr1584_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