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Detailed information for vg0921766254:

Variant ID: vg0921766254 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 21766254
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: 101. )

Flanking Sequence (100 bp) in Reference Genome:

CGACCGGCGGCGGCGGCAGCTAGGCTAGGGTTCGAGTGGAGGCGCACGGGAGAGGAGTAGAGATGAAAATGCTTTAGGGGCAATTTAGTCATTTTCATAC[G/A]
TGGGTCCCACATGTCATAGCTCATTCTCTAACAGAAGGTGGATGGAATGGCACACGGGTAAACGAAATTTTGTGTCATGGCATACAGGTGACTCAAAACT

Reverse complement sequence

AGTTTTGAGTCACCTGTATGCCATGACACAAAATTTCGTTTACCCGTGTGCCATTCCATCCACCTTCTGTTAGAGAATGAGCTATGACATGTGGGACCCA[C/T]
GTATGAAAATGACTAAATTGCCCCTAAAGCATTTTCATCTCTACTCCTCTCCCGTGCGCCTCCACTCGAACCCTAGCCTAGCTGCCGCCGCCGCCGGTCG

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	45.50%	0.50%	0.47%	53.51%	NA
All Indica	2759	12.70%	0.80%	0.80%	85.68%	NA
All Japonica	1512	99.50%	0.00%	0.00%	0.53%	NA
Aus	269	56.10%	0.40%	0.00%	43.49%	NA
Indica I	595	12.90%	0.00%	0.17%	86.89%	NA
Indica II	465	21.30%	4.10%	1.29%	73.33%	NA
Indica III	913	8.40%	0.00%	0.99%	90.58%	NA
Indica Intermediate	786	12.30%	0.50%	0.76%	86.39%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	86.50%	0.00%	0.00%	13.54%	NA
Intermediate	90	70.00%	0.00%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0921766254	G -> DEL	N	N	silent_mutation	Average:39.545; most accessible tissue: Minghui63 root, score: 84.198	N	N	N	N
vg0921766254	G -> A	LOC_Os09g37780.1	upstream_gene_variant ; 894.0bp to feature; MODIFIER	silent_mutation	Average:39.545; most accessible tissue: Minghui63 root, score: 84.198	N	N	N	N
vg0921766254	G -> A	LOC_Os09g37780-LOC_Os09g37790	intergenic_region ; MODIFIER	silent_mutation	Average:39.545; most accessible tissue: Minghui63 root, score: 84.198	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0921766254	4.79E-06	NA	mr1995	Ind_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