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Detailed information for vg1224316333:

Variant ID: vg1224316333 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24316333
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

AATTTTGCCAGTTAATATCAAATAAAAACGAAAGCACAGTTGCAAATTTTTGTTCATTAACTGTTGTCCTTAAGACAGCCAATTTTGCATAGCTTGCAAA[G/A]
AAATTGCTCTGCCATTAAAGGATTCTAAATTTAGCACAGTTTGGTTGTGCTGATCGTTTCAACAGATTAGAAGGAGTAAGAAGGTAAATGCATAACTGAA

Reverse complement sequence

TTCAGTTATGCATTTACCTTCTTACTCCTTCTAATCTGTTGAAACGATCAGCACAACCAAACTGTGCTAAATTTAGAATCCTTTAATGGCAGAGCAATTT[C/T]
TTTGCAAGCTATGCAAAATTGGCTGTCTTAAGGACAACAGTTAATGAACAAAAATTTGCAACTGTGCTTTCGTTTTTATTTGATATTAACTGGCAAAATT

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	97.80%	1.90%	0.25%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	93.30%	6.00%	0.79%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	91.00%	7.60%	1.43%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	87.10%	12.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg1224316333	G -> A	LOC_Os12g39460.1	downstream_gene_variant ; 4299.0bp to feature; MODIFIER	silent_mutation	Average:36.576; most accessible tissue: Zhenshan97 young leaf, score: 64.747	N	N	N	N
vg1224316333	G -> A	LOC_Os12g39450.1	intron_variant ; MODIFIER	silent_mutation	Average:36.576; most accessible tissue: Zhenshan97 young leaf, score: 64.747	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224316333	2.63E-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