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Detailed information for vg0628687836:

Variant ID: vg0628687836 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 28687836
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, A: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

ATTAGCCTTTTTGTTGAAAAATAGATTAATATGATTTTTTAAATCAACTTTTGTGTAGATTTTTTTTGCAAAAAATGCACTGTTTAATAATTTGGTAAAC[G/A]
TGCACGCGGAAAACGAGGGAAGTGAGTTGGGAACCTGCAGGAACGAACGCATCCTTAGTCAGATGTGTCCTATATGAGAGAAAATTCTATTTATGGGCGG

Reverse complement sequence

CCGCCCATAAATAGAATTTTCTCTCATATAGGACACATCTGACTAAGGATGCGTTCGTTCCTGCAGGTTCCCAACTCACTTCCCTCGTTTTCCGCGTGCA[C/T]
GTTTACCAAATTATTAAACAGTGCATTTTTTGCAAAAAAAATCTACACAAAAGTTGATTTAAAAAATCATATTAATCTATTTTTCAACAAAAAGGCTAAT

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	91.00%	8.30%	0.68%	0.00%	NA
All Indica	2759	84.90%	14.00%	1.05%	0.00%	NA
All Japonica	1512	99.70%	0.20%	0.07%	0.00%	NA
Aus	269	98.90%	0.70%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	63.40%	33.50%	3.01%	0.00%	NA
Indica III	913	83.90%	15.60%	0.55%	0.00%	NA
Indica Intermediate	786	87.40%	11.30%	1.27%	0.00%	NA
Temperate Japonica	767	99.60%	0.30%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	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
vg0628687836	G -> A	LOC_Os06g47320.1	upstream_gene_variant ; 758.0bp to feature; MODIFIER	silent_mutation	Average:49.289; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0628687836	G -> A	LOC_Os06g47330.1	upstream_gene_variant ; 958.0bp to feature; MODIFIER	silent_mutation	Average:49.289; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0628687836	G -> A	LOC_Os06g47330.2	upstream_gene_variant ; 1001.0bp to feature; MODIFIER	silent_mutation	Average:49.289; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0628687836	G -> A	LOC_Os06g47320-LOC_Os06g47330	intergenic_region ; MODIFIER	silent_mutation	Average:49.289; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0628687836	NA	3.99E-06	mr1600	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
vg0628687836	2.32E-06	2.32E-06	mr1853	Ind_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
vg0628687836	NA	5.74E-06	mr1050_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
vg0628687836	6.76E-06	NA	mr1361_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
vg0628687836	NA	6.97E-06	mr1361_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