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Detailed information for vg0505023459:

Variant ID: vg0505023459 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5023459
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

AACCACAGTATATCTTACGGTTTTCATAGTAATAACCACATGTTTACCACGATAACCGCCAATCCATAGAGTAACGGTAACCCCACCAAAAACGGTTTGA[G/A]
AAACCTTGGTACACACTGCTAGTGACTATATAAAACGAGATAATTATGGGTGATGATATTTATTTTAATTAGAAGTTTAGGTGTTTTTTGTGTTCTAAAA

Reverse complement sequence

TTTTAGAACACAAAAAACACCTAAACTTCTAATTAAAATAAATATCATCACCCATAATTATCTCGTTTTATATAGTCACTAGCAGTGTGTACCAAGGTTT[C/T]
TCAAACCGTTTTTGGTGGGGTTACCGTTACTCTATGGATTGGCGGTTATCGTGGTAAACATGTGGTTATTACTATGAAAACCGTAAGATATACTGTGGTT

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	72.00%	23.80%	3.70%	0.51%	NA
All Indica	2759	53.50%	40.20%	5.55%	0.76%	NA
All Japonica	1512	98.60%	0.30%	1.06%	0.07%	NA
Aus	269	97.40%	1.10%	1.49%	0.00%	NA
Indica I	595	79.80%	12.30%	7.56%	0.34%	NA
Indica II	465	31.20%	60.20%	7.31%	1.29%	NA
Indica III	913	46.70%	50.50%	1.86%	0.99%	NA
Indica Intermediate	786	54.60%	37.70%	7.25%	0.51%	NA
Temperate Japonica	767	98.20%	0.30%	1.43%	0.13%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	98.30%	0.00%	1.66%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	8.90%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0505023459	G -> DEL	N	N	silent_mutation	Average:70.14; most accessible tissue: Callus, score: 87.332	N	N	N	N
vg0505023459	G -> A	LOC_Os05g09040.1	upstream_gene_variant ; 4423.0bp to feature; MODIFIER	silent_mutation	Average:70.14; most accessible tissue: Callus, score: 87.332	N	N	N	N
vg0505023459	G -> A	LOC_Os05g09050.1	downstream_gene_variant ; 1632.0bp to feature; MODIFIER	silent_mutation	Average:70.14; most accessible tissue: Callus, score: 87.332	N	N	N	N
vg0505023459	G -> A	LOC_Os05g09040-LOC_Os05g09050	intergenic_region ; MODIFIER	silent_mutation	Average:70.14; most accessible tissue: Callus, score: 87.332	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505023459	NA	2.47E-08	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
vg0505023459	9.37E-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
vg0505023459	1.35E-13	3.53E-24	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
vg0505023459	NA	5.93E-06	mr1330	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
vg0505023459	NA	6.46E-11	mr1319_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
vg0505023459	NA	7.28E-07	mr1319_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
vg0505023459	NA	6.43E-13	mr1330_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