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Detailed information for vg0407110892:

Variant ID: vg0407110892 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7110892
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, A: 0.29, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

GGAAAGTCTCCAAGTGTCGTTTGATTAGCACACAGGAAAAACGCAGGAATCTTAGACACATGCCCCTTTGAATCGTAGGGTAGAAAAAACGGAGGAATAG[A/G]
AAAAACACAGTATTCTGACAGGAATTGAAGTATAAAACAGAGGATTGTAAAATACAGGAAAAACACAGGAATGATCGTTTGATTGGAGCACAAGAAAAAC

Reverse complement sequence

GTTTTTCTTGTGCTCCAATCAAACGATCATTCCTGTGTTTTTCCTGTATTTTACAATCCTCTGTTTTATACTTCAATTCCTGTCAGAATACTGTGTTTTT[T/C]
CTATTCCTCCGTTTTTTCTACCCTACGATTCAAAGGGGCATGTGTCTAAGATTCCTGCGTTTTTCCTGTGTGCTAATCAAACGACACTTGGAGACTTTCC

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	28.00%	18.20%	0.68%	53.15%	NA
All Indica	2759	32.70%	1.60%	0.98%	64.70%	NA
All Japonica	1512	15.70%	50.10%	0.26%	33.86%	NA
Aus	269	42.80%	0.00%	0.00%	57.25%	NA
Indica I	595	20.50%	2.40%	1.51%	75.63%	NA
Indica II	465	42.20%	2.40%	1.29%	54.19%	NA
Indica III	913	34.00%	0.50%	0.22%	65.28%	NA
Indica Intermediate	786	34.90%	1.90%	1.27%	61.96%	NA
Temperate Japonica	767	23.60%	74.70%	0.13%	1.56%	NA
Tropical Japonica	504	5.60%	7.50%	0.20%	86.71%	NA
Japonica Intermediate	241	12.00%	61.00%	0.83%	26.14%	NA
VI/Aromatic	96	40.60%	34.40%	0.00%	25.00%	NA
Intermediate	90	32.20%	25.60%	1.11%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0407110892	A -> DEL	N	N	silent_mutation	Average:21.224; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg0407110892	A -> G	LOC_Os04g12864.1	upstream_gene_variant ; 423.0bp to feature; MODIFIER	silent_mutation	Average:21.224; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg0407110892	A -> G	LOC_Os04g12850-LOC_Os04g12864	intergenic_region ; MODIFIER	silent_mutation	Average:21.224; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0407110892	5.52E-07	NA	mr1035	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
vg0407110892	NA	4.12E-06	mr1608	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
vg0407110892	2.13E-06	NA	mr1626	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
vg0407110892	NA	9.55E-06	mr1919	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
vg0407110892	NA	9.37E-06	mr1035_2	Jap_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
vg0407110892	NA	1.51E-08	mr1631_2	Jap_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
vg0407110892	NA	6.98E-08	mr1846_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