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Detailed information for vg0823317285:

Variant ID: vg0823317285 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 23317285
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTTATTTTTTTCATAATTTCTTTAAATAAGTGTCACGCCCCGAACTAGTCCCGACCGGAACTAGCCCGTGACGCTCCAAATTAACCTGTTAATCAAT[A/G]
CCAGTCCCAGGAAACAGTGCTGGTATCACAGGGAGACAGAATATCACAGCATCAGAGGTCTCTTTATTATAGAGTAGAGGTACAGTCATGTTGGGCTGCG

Reverse complement sequence

CGCAGCCCAACATGACTGTACCTCTACTCTATAATAAAGAGACCTCTGATGCTGTGATATTCTGTCTCCCTGTGATACCAGCACTGTTTCCTGGGACTGG[T/C]
ATTGATTAACAGGTTAATTTGGAGCGTCACGGGCTAGTTCCGGTCGGGACTAGTTCGGGGCGTGACACTTATTTAAAGAAATTATGAAAAAAATAAAAAA

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	34.40%	0.10%	8.82%	56.69%	NA
All Indica	2759	2.60%	0.20%	8.55%	88.58%	NA
All Japonica	1512	98.60%	0.00%	0.00%	1.39%	NA
Aus	269	4.80%	0.00%	58.74%	36.43%	NA
Indica I	595	1.30%	0.20%	0.17%	98.32%	NA
Indica II	465	2.60%	0.60%	13.33%	83.44%	NA
Indica III	913	1.80%	0.00%	8.87%	89.38%	NA
Indica Intermediate	786	4.70%	0.30%	11.70%	83.33%	NA
Temperate Japonica	767	98.40%	0.00%	0.00%	1.56%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	97.50%	0.00%	0.00%	2.49%	NA
VI/Aromatic	96	7.30%	0.00%	19.79%	72.92%	NA
Intermediate	90	44.40%	0.00%	4.44%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0823317285	A -> G	LOC_Os08g36890-LOC_Os08g36900	intergenic_region ; MODIFIER	silent_mutation	Average:28.736; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0823317285	A -> DEL	N	N	silent_mutation	Average:28.736; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0823317285	1.84E-06	NA	Grain_weight	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