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Detailed information for vg1224314963:

Variant ID: vg1224314963 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24314963
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.02, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

GGTTGGCCTAGGAGGCATCAGAAATCCTTTGAAATCTTTGAAGGTAAACTTATGTTGCCTCGATCACTTTCGCCTTAGTTTCAGCCAAAATCTGACTTAA[G/A]
TTTGTTAAACATGGTGGATGTGCACTCACTAACAGTTTGCATCCTGCAGTGCGTTGGAATAGCAGAAAGTAAGCGTGAGACAGTCCATAAAACCGTGGAG

Reverse complement sequence

CTCCACGGTTTTATGGACTGTCTCACGCTTACTTTCTGCTATTCCAACGCACTGCAGGATGCAAACTGTTAGTGAGTGCACATCCACCATGTTTAACAAA[C/T]
TTAAGTCAGATTTTGGCTGAAACTAAGGCGAAAGTGATCGAGGCAACATAAGTTTACCTTCAAAGATTTCAAAGGATTTCTGATGCCTCCTAGGCCAACC

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	58.30%	41.00%	0.36%	0.38%	NA
All Indica	2759	44.00%	55.30%	0.04%	0.65%	NA
All Japonica	1512	92.10%	6.90%	0.99%	0.00%	NA
Aus	269	0.70%	99.30%	0.00%	0.00%	NA
Indica I	595	35.00%	65.00%	0.00%	0.00%	NA
Indica II	465	46.00%	52.70%	0.00%	1.29%	NA
Indica III	913	57.80%	41.70%	0.00%	0.44%	NA
Indica Intermediate	786	33.60%	65.30%	0.13%	1.02%	NA
Temperate Japonica	767	89.40%	8.70%	1.83%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	85.90%	13.70%	0.41%	0.00%	NA
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	66.70%	32.20%	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
vg1224314963	G -> DEL	N	N	silent_mutation	Average:60.367; most accessible tissue: Callus, score: 79.928	N	N	N	N
vg1224314963	G -> A	LOC_Os12g39450.1	upstream_gene_variant ; 205.0bp to feature; MODIFIER	silent_mutation	Average:60.367; most accessible tissue: Callus, score: 79.928	N	N	N	N
vg1224314963	G -> A	LOC_Os12g39440-LOC_Os12g39450	intergenic_region ; MODIFIER	silent_mutation	Average:60.367; most accessible tissue: Callus, score: 79.928	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224314963	NA	7.70E-07	mr1066	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
vg1224314963	2.95E-06	NA	mr1627	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