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Detailed information for vg0825345819:

Variant ID: vg0825345819 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25345819
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 377. )

Flanking Sequence (100 bp) in Reference Genome:

TGATGGCATGGACAAGCATGATCATCGGCTTAGCTAAGCATGGCCATGGCAAGGATGCTGTGCAACTCTTCAACCAAATGCAGCATGGTGGTGTTGTTCC[G/A]
GATCATGTTGCATTTGTAGGTGTTCTTACTGCTTGCAGCCATGCTGGGATGGTAGACGAAGCAAGAAAATACTTTGACTCCATGTGGAATCATTATGGCA

Reverse complement sequence

TGCCATAATGATTCCACATGGAGTCAAAGTATTTTCTTGCTTCGTCTACCATCCCAGCATGGCTGCAAGCAGTAAGAACACCTACAAATGCAACATGATC[C/T]
GGAACAACACCACCATGCTGCATTTGGTTGAAGAGTTGCACAGCATCCTTGCCATGGCCATGCTTAGCTAAGCCGATGATCATGCTTGTCCATGCCATCA

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	98.60%	1.40%	0.06%	0.00%	NA
All Indica	2759	99.80%	0.10%	0.04%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.30%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	38.50%	61.50%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0825345819	G -> A	LOC_Os08g40020.1	synonymous_variant ; p.Pro361Pro; LOW	synonymous_codon	Average:64.827; most accessible tissue: Callus, score: 86.972	N	N	N	N