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Detailed information for vg0204738000:

Variant ID: vg0204738000 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 4738000
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.53, A: 0.47, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:

CACCTTCCTCTCGATATAGCCCATGATCTCGTAGCTACTATGTAGTAATATGTTTACTGATATGTTCAGTACACTGTATAAGAGTAAAAGCTGAGACTTC[G/A]
TGGTCTGCGAGTAAAACAATTACTACTTTTCTCTCGATATAGCTCATGATCTCGTAGCAACCATATAGTAATATGTTTACTGATGTATTCAATACACGGT

Reverse complement sequence

ACCGTGTATTGAATACATCAGTAAACATATTACTATATGGTTGCTACGAGATCATGAGCTATATCGAGAGAAAAGTAGTAATTGTTTTACTCGCAGACCA[C/T]
GAAGTCTCAGCTTTTACTCTTATACAGTGTACTGAACATATCAGTAAACATATTACTACATAGTAGCTACGAGATCATGGGCTATATCGAGAGGAAGGTG

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	68.20%	7.60%	7.68%	16.50%	NA
All Indica	2759	53.30%	10.10%	8.55%	28.09%	NA
All Japonica	1512	87.60%	4.40%	7.94%	0.07%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	55.60%	3.70%	8.74%	31.93%	NA
Indica II	465	62.60%	11.00%	5.16%	21.29%	NA
Indica III	913	46.80%	15.00%	9.97%	28.26%	NA
Indica Intermediate	786	53.60%	8.70%	8.78%	29.01%	NA
Temperate Japonica	767	76.50%	8.50%	14.86%	0.13%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	97.10%	0.80%	2.07%	0.00%	NA
VI/Aromatic	96	95.80%	2.10%	2.08%	0.00%	NA
Intermediate	90	83.30%	6.70%	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
vg0204738000	G -> A	LOC_Os02g09220.1	upstream_gene_variant ; 2044.0bp to feature; MODIFIER	silent_mutation	Average:22.801; most accessible tissue: Callus, score: 41.533	N	N	N	N
vg0204738000	G -> A	LOC_Os02g09210-LOC_Os02g09220	intergenic_region ; MODIFIER	silent_mutation	Average:22.801; most accessible tissue: Callus, score: 41.533	N	N	N	N
vg0204738000	G -> DEL	N	N	silent_mutation	Average:22.801; most accessible tissue: Callus, score: 41.533	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0204738000	2.90E-09	9.69E-12	mr1588_2	Jap_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