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Detailed information for vg0628648301:

Variant ID: vg0628648301 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 28648301
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

AAACAGTTTCAAGTTGGAAGTTGACAAAAAAATATATACTCCCCACGTTTCAGGATATAAGACGTTTTCACTTTGATTAAAGTCAAACTGTTTTAAGCCT[G/A]
ATCAAATTTATAGAAAAAAGTAGTAACATTTTCAACCTAAGACAAATCTATTATGAAAATTTATTTAATTATTAATTTGATGAAACTAATTTAGTATTAT

Reverse complement sequence

ATAATACTAAATTAGTTTCATCAAATTAATAATTAAATAAATTTTCATAATAGATTTGTCTTAGGTTGAAAATGTTACTACTTTTTTCTATAAATTTGAT[C/T]
AGGCTTAAAACAGTTTGACTTTAATCAAAGTGAAAACGTCTTATATCCTGAAACGTGGGGAGTATATATTTTTTTGTCAACTTCCAACTTGAAACTGTTT

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	69.40%	30.20%	0.36%	0.00%	NA
All Indica	2759	51.30%	48.50%	0.29%	0.00%	NA
All Japonica	1512	96.20%	3.20%	0.60%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	66.70%	33.10%	0.17%	0.00%	NA
Indica II	465	28.40%	71.20%	0.43%	0.00%	NA
Indica III	913	53.00%	46.70%	0.33%	0.00%	NA
Indica Intermediate	786	51.00%	48.70%	0.25%	0.00%	NA
Temperate Japonica	767	92.70%	6.10%	1.17%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	62.20%	37.80%	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
vg0628648301	G -> A	LOC_Os06g47260.1	upstream_gene_variant ; 2769.0bp to feature; MODIFIER	silent_mutation	Average:52.207; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0628648301	G -> A	LOC_Os06g47270.1	upstream_gene_variant ; 4492.0bp to feature; MODIFIER	silent_mutation	Average:52.207; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0628648301	G -> A	LOC_Os06g47260.2	upstream_gene_variant ; 2769.0bp to feature; MODIFIER	silent_mutation	Average:52.207; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0628648301	G -> A	LOC_Os06g47250.1	intron_variant ; MODIFIER	silent_mutation	Average:52.207; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0628648301	7.63E-06	NA	mr1245_2	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
vg0628648301	3.28E-07	9.51E-09	mr1321_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
vg0628648301	5.10E-06	6.69E-08	mr1974_2	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
vg0628648301	NA	2.77E-06	mr1974_2	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