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Detailed information for vg0412964994:

Variant ID: vg0412964994 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12964994
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

AATAGAGAGGGAGGGTGAGGCCTCCCGGTATCATTTTAGAGAGCATTGAGTTGTAAGAATAGCTAGGGTTTCGAGTTTAGTAGAGATTTTCTTTAGGAGT[G/A]
TTGTTGTTGCACTTTCTAAACACAGAGATAAGTAATAAAGTTGTCATCTACATCAAGAGTTCTTTGATTTGTGTTTGCTCGGGTTCAGCGGTCTAACCGG

Reverse complement sequence

CCGGTTAGACCGCTGAACCCGAGCAAACACAAATCAAAGAACTCTTGATGTAGATGACAACTTTATTACTTATCTCTGTGTTTAGAAAGTGCAACAACAA[C/T]
ACTCCTAAAGAAAATCTCTACTAAACTCGAAACCCTAGCTATTCTTACAACTCAATGCTCTCTAAAATGATACCGGGAGGCCTCACCCTCCCTCTCTATT

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	56.60%	43.10%	0.11%	0.19%	NA
All Indica	2759	27.00%	72.50%	0.18%	0.33%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	16.30%	83.40%	0.34%	0.00%	NA
Indica II	465	15.30%	84.30%	0.00%	0.43%	NA
Indica III	913	40.00%	59.70%	0.00%	0.33%	NA
Indica Intermediate	786	27.00%	72.10%	0.38%	0.51%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	67.80%	32.20%	0.00%	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
vg0412964994	G -> DEL	N	N	silent_mutation	Average:47.32; most accessible tissue: Zhenshan97 young leaf, score: 69.723	N	N	N	N
vg0412964994	G -> A	LOC_Os04g22870-LOC_Os04g22880	intergenic_region ; MODIFIER	silent_mutation	Average:47.32; most accessible tissue: Zhenshan97 young leaf, score: 69.723	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412964994	NA	1.39E-10	mr1946	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