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Detailed information for vg1224152951:

Variant ID: vg1224152951 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24152951
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.82, A: 0.19, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

GTGATGTACTTATATATTCTAAATAGAAACCTAGAACAATCACGGTTGTTATTGTGGTCCGAAAAGAAAAAATATCAGACATTATTGCAGCTTGACATGC[G/A]
CAATATAGTGACCACTGATTTGTACAAAGGTTTGAAATTTCAAAGTTAAACATGTCATTTTCAATTTTTTAGAGATAATCCGAGAAATGCCATTGACAAG

Reverse complement sequence

CTTGTCAATGGCATTTCTCGGATTATCTCTAAAAAATTGAAAATGACATGTTTAACTTTGAAATTTCAAACCTTTGTACAAATCAGTGGTCACTATATTG[C/T]
GCATGTCAAGCTGCAATAATGTCTGATATTTTTTCTTTTCGGACCACAATAACAACCGTGATTGTTCTAGGTTTCTATTTAGAATATATAAGTACATCAC

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	92.00%	7.00%	0.95%	0.00%	NA
All Indica	2759	86.90%	11.70%	1.41%	0.00%	NA
All Japonica	1512	99.40%	0.30%	0.33%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.30%	0.20%	1.51%	0.00%	NA
Indica II	465	71.60%	25.60%	2.80%	0.00%	NA
Indica III	913	86.60%	12.70%	0.66%	0.00%	NA
Indica Intermediate	786	87.70%	10.90%	1.40%	0.00%	NA
Temperate Japonica	767	99.30%	0.30%	0.39%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.40%	0.83%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	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
vg1224152951	G -> A	LOC_Os12g39230.1	upstream_gene_variant ; 2438.0bp to feature; MODIFIER	silent_mutation	Average:32.575; most accessible tissue: Callus, score: 51.125	N	N	N	N
vg1224152951	G -> A	LOC_Os12g39300.1	downstream_gene_variant ; 1847.0bp to feature; MODIFIER	silent_mutation	Average:32.575; most accessible tissue: Callus, score: 51.125	N	N	N	N
vg1224152951	G -> A	LOC_Os12g39240.1	downstream_gene_variant ; 1985.0bp to feature; MODIFIER	silent_mutation	Average:32.575; most accessible tissue: Callus, score: 51.125	N	N	N	N
vg1224152951	G -> A	LOC_Os12g39230-LOC_Os12g39300	intergenic_region ; MODIFIER	silent_mutation	Average:32.575; most accessible tissue: Callus, score: 51.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224152951	4.95E-06	NA	mr1632	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
vg1224152951	NA	9.65E-06	mr1632	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