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Detailed information for vg1214515514:

Variant ID: vg1214515514 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14515514
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: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TCAGGCCAGAAGCATGTTAGTTATGCCAGCAGTAGAACTGACGGGGAAGTAGTCAAGAGTTAGTAAGATCAGGAGCTAAATGAGAATTTCTTTATGAGGA[G/A]
TTTCCTATCAACAACTGAGGGTTAAGTTCCAAGTCTTGTCCTGGATGAAAGTGCATCGTCATTGCTTTATTTTGATTGATCGATGAAGTTTTCTATTTTC

Reverse complement sequence

GAAAATAGAAAACTTCATCGATCAATCAAAATAAAGCAATGACGATGCACTTTCATCCAGGACAAGACTTGGAACTTAACCCTCAGTTGTTGATAGGAAA[C/T]
TCCTCATAAAGAAATTCTCATTTAGCTCCTGATCTTACTAACTCTTGACTACTTCCCCGTCAGTTCTACTGCTGGCATAACTAACATGCTTCTGGCCTGA

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	59.40%	4.00%	16.12%	20.48%	NA
All Indica	2759	40.20%	6.30%	25.41%	28.09%	NA
All Japonica	1512	92.30%	0.30%	0.73%	6.75%	NA
Aus	269	53.20%	2.20%	14.87%	29.74%	NA
Indica I	595	67.40%	1.70%	22.69%	8.24%	NA
Indica II	465	40.00%	11.00%	20.43%	28.60%	NA
Indica III	913	21.80%	8.50%	29.68%	39.98%	NA
Indica Intermediate	786	41.00%	4.60%	25.45%	29.01%	NA
Temperate Japonica	767	90.50%	0.30%	0.52%	8.74%	NA
Tropical Japonica	504	96.80%	0.20%	0.40%	2.58%	NA
Japonica Intermediate	241	88.40%	0.40%	2.07%	9.13%	NA
VI/Aromatic	96	94.80%	3.10%	1.04%	1.04%	NA
Intermediate	90	77.80%	1.10%	10.00%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214515514	G -> DEL	N	N	silent_mutation	Average:33.875; most accessible tissue: Callus, score: 71.287	N	N	N	N
vg1214515514	G -> A	LOC_Os12g25240.1	upstream_gene_variant ; 1785.0bp to feature; MODIFIER	silent_mutation	Average:33.875; most accessible tissue: Callus, score: 71.287	N	N	N	N
vg1214515514	G -> A	LOC_Os12g25250.1	upstream_gene_variant ; 3852.0bp to feature; MODIFIER	silent_mutation	Average:33.875; most accessible tissue: Callus, score: 71.287	N	N	N	N
vg1214515514	G -> A	LOC_Os12g25230.1	downstream_gene_variant ; 1164.0bp to feature; MODIFIER	silent_mutation	Average:33.875; most accessible tissue: Callus, score: 71.287	N	N	N	N
vg1214515514	G -> A	LOC_Os12g25230-LOC_Os12g25240	intergenic_region ; MODIFIER	silent_mutation	Average:33.875; most accessible tissue: Callus, score: 71.287	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214515514	4.75E-06	NA	mr1264	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
vg1214515514	8.47E-06	NA	mr1264	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
vg1214515514	2.26E-06	NA	mr1655	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