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Detailed information for vg0704593889:

Variant ID: vg0704593889 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 4593889
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTATCACCTTCGCAGCAGAAACCAATCAGTTTGATTAGGTTGATATGTTGGGTCATTCCAATTGAGCTCACTTCTGCCCTGAATTGCTTCTCTCCCTG[A/G]
CGAGCACCATCAAGCCTTTTCACTGCTATAGCAGTCTGGTCTCCCAACATTCCCTTGAATACAGAACCAAAACCACCTCCTCCTAGCTTCTCTGAGAAAC

Reverse complement sequence

GTTTCTCAGAGAAGCTAGGAGGAGGTGGTTTTGGTTCTGTATTCAAGGGAATGTTGGGAGACCAGACTGCTATAGCAGTGAAAAGGCTTGATGGTGCTCG[T/C]
CAGGGAGAGAAGCAATTCAGGGCAGAAGTGAGCTCAATTGGAATGACCCAACATATCAACCTAATCAAACTGATTGGTTTCTGCTGCGAAGGTGATAAGA

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	99.50%	0.50%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	93.30%	6.70%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0704593889	A -> G	LOC_Os07g08860.1	synonymous_variant ; p.Arg573Arg; LOW	synonymous_codon	Average:53.248; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N