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Detailed information for vg0803417672:

Variant ID: vg0803417672 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 3417672
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.65, A: 0.34, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

CCAATTGCACAGTTTGCATATAAATTATGAGACGAATCTTTTGAGCCTAATTACGCCATGATTTGACAATGTGGTGCTACAGTAAACATTTGCTAATGAC[A/G]
GATTAATTATGCTTAATAAATTCGTCTCGCAGTTTATACGTGGAATCTGTAATTTGTTTTGTTATTAGACTACATTTAATATTTTAAATGTGTGTCCGTA

Reverse complement sequence

TACGGACACACATTTAAAATATTAAATGTAGTCTAATAACAAAACAAATTACAGATTCCACGTATAAACTGCGAGACGAATTTATTAAGCATAATTAATC[T/C]
GTCATTAGCAAATGTTTACTGTAGCACCACATTGTCAAATCATGGCGTAATTAGGCTCAAAAGATTCGTCTCATAATTTATATGCAAACTGTGCAATTGG

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	50.40%	47.40%	2.18%	0.00%	NA
All Indica	2759	31.70%	64.60%	3.70%	0.00%	NA
All Japonica	1512	95.00%	4.90%	0.07%	0.00%	NA
Aus	269	2.60%	97.40%	0.00%	0.00%	NA
Indica I	595	52.30%	39.00%	8.74%	0.00%	NA
Indica II	465	71.20%	26.50%	2.37%	0.00%	NA
Indica III	913	0.20%	99.20%	0.55%	0.00%	NA
Indica Intermediate	786	29.40%	66.30%	4.33%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	86.90%	12.90%	0.20%	0.00%	NA
Japonica Intermediate	241	97.10%	2.90%	0.00%	0.00%	NA
VI/Aromatic	96	13.50%	86.50%	0.00%	0.00%	NA
Intermediate	90	54.40%	45.60%	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
vg0803417672	A -> G	LOC_Os08g06180.1	upstream_gene_variant ; 4278.0bp to feature; MODIFIER	silent_mutation	Average:58.936; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N
vg0803417672	A -> G	LOC_Os08g06190.1	upstream_gene_variant ; 501.0bp to feature; MODIFIER	silent_mutation	Average:58.936; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N
vg0803417672	A -> G	LOC_Os08g06200.1	upstream_gene_variant ; 2897.0bp to feature; MODIFIER	silent_mutation	Average:58.936; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N
vg0803417672	A -> G	LOC_Os08g06190-LOC_Os08g06200	intergenic_region ; MODIFIER	silent_mutation	Average:58.936; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0803417672	NA	5.73E-07	mr1063	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
vg0803417672	9.97E-08	9.97E-08	mr1194	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
vg0803417672	NA	1.28E-09	mr1277	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
vg0803417672	NA	3.26E-08	mr1352	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
vg0803417672	8.29E-06	NA	mr1375	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
vg0803417672	NA	6.78E-07	mr1870	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