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Detailed information for vg1204256697:

Variant ID: vg1204256697 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4256697
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.18, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

CATTATTCTCTAAGTACAAGTAGAACTATATTATTCTAAAACAAATATGCATTATAAGTGTAGCTAGTTCTCATATTGACGGTCGAAATTGGTCTATAAC[A/G]
ACCATCAACATTGCCGCCATCCCTGTCGCCGGCCGCTCATTTGCGTCGCGTTGTCCGCTCCCGCTGCCCTCGCCGCTCCCACCGTCGGGGAAGGTGGATC

Reverse complement sequence

GATCCACCTTCCCCGACGGTGGGAGCGGCGAGGGCAGCGGGAGCGGACAACGCGACGCAAATGAGCGGCCGGCGACAGGGATGGCGGCAATGTTGATGGT[T/C]
GTTATAGACCAATTTCGACCGTCAATATGAGAACTAGCTACACTTATAATGCATATTTGTTTTAGAATAATATAGTTCTACTTGTACTTAGAGAATAATG

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	40.90%	35.10%	0.23%	23.83%	NA
All Indica	2759	64.30%	25.40%	0.29%	10.00%	NA
All Japonica	1512	2.70%	55.40%	0.07%	41.80%	NA
Aus	269	29.40%	23.80%	0.37%	46.47%	NA
Indica I	595	83.40%	11.60%	0.17%	4.87%	NA
Indica II	465	61.90%	25.20%	0.65%	12.26%	NA
Indica III	913	55.90%	31.80%	0.22%	12.16%	NA
Indica Intermediate	786	61.10%	28.60%	0.25%	10.05%	NA
Temperate Japonica	767	2.70%	79.40%	0.13%	17.73%	NA
Tropical Japonica	504	2.40%	28.80%	0.00%	68.85%	NA
Japonica Intermediate	241	3.30%	34.90%	0.00%	61.83%	NA
VI/Aromatic	96	7.30%	18.80%	0.00%	73.96%	NA
Intermediate	90	34.40%	40.00%	1.11%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204256697	A -> DEL	N	N	silent_mutation	Average:68.691; most accessible tissue: Zhenshan97 flag leaf, score: 76.356	N	N	N	N
vg1204256697	A -> G	LOC_Os12g08360.1	downstream_gene_variant ; 1563.0bp to feature; MODIFIER	silent_mutation	Average:68.691; most accessible tissue: Zhenshan97 flag leaf, score: 76.356	N	N	N	N
vg1204256697	A -> G	LOC_Os12g08370.1	downstream_gene_variant ; 3085.0bp to feature; MODIFIER	silent_mutation	Average:68.691; most accessible tissue: Zhenshan97 flag leaf, score: 76.356	N	N	N	N
vg1204256697	A -> G	LOC_Os12g08360-LOC_Os12g08370	intergenic_region ; MODIFIER	silent_mutation	Average:68.691; most accessible tissue: Zhenshan97 flag leaf, score: 76.356	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204256697	NA	1.05E-06	mr1111_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
vg1204256697	1.31E-06	1.31E-06	mr1448_2	Jap_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