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Detailed information for vg1224668311:

Variant ID: vg1224668311 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24668311
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.02, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

ATACTTGTATCTTCAACAAATAGCTTGTGCAGTTGTGCTACACTAAGAAATTATTAAAGAACTCACATGAATATATAATGAAATACTTATATCTTCGACT[A/G]
TACCCTTCTTTCTTTGGATAATGAAATACTAGTAGATGAATACTCCTAGACAGGTGAGAATAATTAATTACTAGACCAGTGAACACGCTCAACTCAAGGT

Reverse complement sequence

ACCTTGAGTTGAGCGTGTTCACTGGTCTAGTAATTAATTATTCTCACCTGTCTAGGAGTATTCATCTACTAGTATTTCATTATCCAAAGAAAGAAGGGTA[T/C]
AGTCGAAGATATAAGTATTTCATTATATATTCATGTGAGTTCTTTAATAATTTCTTAGTGTAGCACAACTGCACAAGCTATTTGTTGAAGATACAAGTAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.20%	17.30%	3.49%	0.00%	NA
All Indica	2759	65.10%	29.20%	5.69%	0.00%	NA
All Japonica	1512	99.40%	0.40%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	88.90%	5.00%	6.05%	0.00%	NA
Indica II	465	38.50%	51.20%	10.32%	0.00%	NA
Indica III	913	58.60%	38.60%	2.85%	0.00%	NA
Indica Intermediate	786	70.40%	23.70%	5.98%	0.00%	NA
Temperate Japonica	767	99.00%	0.70%	0.39%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	6.70%	5.56%	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
vg1224668311	A -> G	LOC_Os12g39920.1	downstream_gene_variant ; 1469.0bp to feature; MODIFIER	silent_mutation	Average:46.113; most accessible tissue: Callus, score: 85.775	N	N	N	N
vg1224668311	A -> G	LOC_Os12g39910-LOC_Os12g39920	intergenic_region ; MODIFIER	silent_mutation	Average:46.113; most accessible tissue: Callus, score: 85.775	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224668311	2.41E-06	2.40E-06	mr1848_2	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