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Detailed information for vg0504890865:

Variant ID: vg0504890865 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 4890865
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: 112. )

Flanking Sequence (100 bp) in Reference Genome:

TCTATGATTTGATAATGTGGTGCTACAGTAAACATTTGCTAATAACAGATTAATTAGACTTAATAAATTCGTCTCGCGGTTTACTGACGGATTTTTTTCT[G/A]
TAATTAGTTTTTTTATTAGTACCTGAACACCCCATGTGATACCCTATATATTATCCGATGTGACACGCCAAAACTTTACACCCCTGGATCAAAATACCCC

Reverse complement sequence

GGGGTATTTTGATCCAGGGGTGTAAAGTTTTGGCGTGTCACATCGGATAATATATAGGGTATCACATGGGGTGTTCAGGTACTAATAAAAAAACTAATTA[C/T]
AGAAAAAAATCCGTCAGTAAACCGCGAGACGAATTTATTAAGTCTAATTAATCTGTTATTAGCAAATGTTTACTGTAGCACCACATTATCAAATCATAGA

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	60.60%	31.60%	1.97%	5.84%	NA
All Indica	2759	43.80%	52.20%	2.94%	1.09%	NA
All Japonica	1512	97.90%	1.50%	0.40%	0.20%	NA
Aus	269	10.80%	2.60%	0.37%	86.25%	NA
Indica I	595	17.10%	74.80%	8.07%	0.00%	NA
Indica II	465	80.00%	17.20%	1.29%	1.51%	NA
Indica III	913	41.50%	57.70%	0.44%	0.33%	NA
Indica Intermediate	786	45.20%	49.40%	2.93%	2.54%	NA
Temperate Japonica	767	97.80%	1.70%	0.52%	0.00%	NA
Tropical Japonica	504	98.20%	1.40%	0.40%	0.00%	NA
Japonica Intermediate	241	97.50%	1.20%	0.00%	1.24%	NA
VI/Aromatic	96	91.70%	1.00%	0.00%	7.29%	NA
Intermediate	90	65.60%	24.40%	5.56%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0504890865	G -> DEL	N	N	silent_mutation	Average:47.362; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0504890865	G -> A	LOC_Os05g08854.1	upstream_gene_variant ; 622.0bp to feature; MODIFIER	silent_mutation	Average:47.362; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0504890865	G -> A	LOC_Os05g08860.1	upstream_gene_variant ; 4176.0bp to feature; MODIFIER	silent_mutation	Average:47.362; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0504890865	G -> A	LOC_Os05g08854.2	upstream_gene_variant ; 622.0bp to feature; MODIFIER	silent_mutation	Average:47.362; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0504890865	G -> A	LOC_Os05g08850.1	downstream_gene_variant ; 2854.0bp to feature; MODIFIER	silent_mutation	Average:47.362; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0504890865	G -> A	LOC_Os05g08854-LOC_Os05g08860	intergenic_region ; MODIFIER	silent_mutation	Average:47.362; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0504890865	NA	6.56E-14	Grain_length	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
vg0504890865	6.46E-07	3.25E-15	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
vg0504890865	8.71E-09	NA	Grain_width	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
vg0504890865	8.43E-13	1.65E-32	Grain_width	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
vg0504890865	NA	5.87E-07	mr1183	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
vg0504890865	NA	9.26E-06	mr1188	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
vg0504890865	NA	1.25E-06	mr1503	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
vg0504890865	NA	1.41E-07	mr1794	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
vg0504890865	NA	1.90E-08	mr1330_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