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Detailed information for vg1116565892:

Variant ID: vg1116565892 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16565892
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, A: 0.30, others allele: 0.00, population size: 168. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGAAAATAATGGCGGTATGTTATTTGCTCGAATTTTACTTAATTTACACATCACTCAAATTGGTGGTCTGTACTTTAAAAATAGCATGAAATTTTGAT[G/A]
CTTCAAACAACTAATTCAATTTGAAGAAGCCAAGCAGGTAAGAATCGAGTGTTTTATTGCGTGTAGTGTGCAACATGCATGTGCTCCCTATATGCTGCAC

Reverse complement sequence

GTGCAGCATATAGGGAGCACATGCATGTTGCACACTACACGCAATAAAACACTCGATTCTTACCTGCTTGGCTTCTTCAAATTGAATTAGTTGTTTGAAG[C/T]
ATCAAAATTTCATGCTATTTTTAAAGTACAGACCACCAATTTGAGTGATGTGTAAATTAAGTAAAATTCGAGCAAATAACATACCGCCATTATTTTCTTT

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	40.00%	14.80%	1.93%	43.21%	NA
All Indica	2759	4.80%	23.30%	2.86%	69.01%	NA
All Japonica	1512	93.60%	0.70%	0.40%	5.29%	NA
Aus	269	83.30%	7.10%	0.37%	9.29%	NA
Indica I	595	2.20%	12.10%	3.70%	82.02%	NA
Indica II	465	1.50%	46.50%	1.51%	50.54%	NA
Indica III	913	3.90%	17.00%	3.18%	75.90%	NA
Indica Intermediate	786	9.70%	25.60%	2.67%	62.09%	NA
Temperate Japonica	767	96.10%	0.70%	0.13%	3.13%	NA
Tropical Japonica	504	88.90%	0.80%	0.60%	9.72%	NA
Japonica Intermediate	241	95.40%	0.80%	0.83%	2.90%	NA
VI/Aromatic	96	90.60%	7.30%	1.04%	1.04%	NA
Intermediate	90	37.80%	22.20%	4.44%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116565892	G -> A	LOC_Os11g28650.1	upstream_gene_variant ; 4414.0bp to feature; MODIFIER	silent_mutation	Average:32.446; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N
vg1116565892	G -> A	LOC_Os11g28640-LOC_Os11g28650	intergenic_region ; MODIFIER	silent_mutation	Average:32.446; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N
vg1116565892	G -> DEL	N	N	silent_mutation	Average:32.446; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116565892	7.23E-06	NA	Grain_thickness	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1116565892	4.00E-06	3.59E-12	Heading_date	Ind_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1116565892	NA	8.32E-13	mr1031	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
vg1116565892	NA	3.19E-13	mr1056	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
vg1116565892	NA	9.33E-32	mr1213	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
vg1116565892	NA	8.95E-09	mr1465	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
vg1116565892	NA	3.57E-07	mr1756	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