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Detailed information for vg1207428614:

Variant ID: vg1207428614 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7428614
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

TTCACAACTCCTGTCTCCTGGTAGCTATGTACCCTCTTAGGCTGAGTTCGTTAGTGGGGGATGGGAACTAATCCCTTTGGCACCTAAAACGGAGCGACTC[G/A]
TTAGCGCATGATTAATTAAGTATTAATCATTTTTAAAGAAAAAAGATTAATAGTATTTTAAAAACGACTTTCACATAGGAAATTTTTGCAAAAAAACATG

Reverse complement sequence

CATGTTTTTTTGCAAAAATTTCCTATGTGAAAGTCGTTTTTAAAATACTATTAATCTTTTTTCTTTAAAAATGATTAATACTTAATTAATCATGCGCTAA[C/T]
GAGTCGCTCCGTTTTAGGTGCCAAAGGGATTAGTTCCCATCCCCCACTAACGAACTCAGCCTAAGAGGGTACATAGCTACCAGGAGACAGGAGTTGTGAA

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	98.50%	0.90%	0.63%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	95.30%	2.80%	1.85%	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%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	91.90%	5.30%	2.74%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	97.50%	0.80%	1.66%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg1207428614	G -> A	LOC_Os12g13320.1	upstream_gene_variant ; 1916.0bp to feature; MODIFIER	silent_mutation	Average:60.925; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N
vg1207428614	G -> A	LOC_Os12g13300.1	downstream_gene_variant ; 904.0bp to feature; MODIFIER	silent_mutation	Average:60.925; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N
vg1207428614	G -> A	LOC_Os12g13300-LOC_Os12g13320	intergenic_region ; MODIFIER	silent_mutation	Average:60.925; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207428614	4.98E-07	NA	mr1002_2	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