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Detailed information for vg0427576821:

Variant ID: vg0427576821 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 27576821
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: 277. )

Flanking Sequence (100 bp) in Reference Genome:

CACGTATGAGACCAACAAAGCAGAGCAATTCGCACGACATGCGGAACGTAGGTTGCAGTGAAACGCATGACTTACGGGCGGAGATGGTGGAGCCGACGGC[G/A]
ATGAACACAAAGAGGAAGGTGGAGAAGAACTCGGCGAAGTACGCCCGGAGCGCCGGCGGCGAGAAGCAGCGCTTCATGTTGGCACAGATGTTCGCCATTG

Reverse complement sequence

CAATGGCGAACATCTGTGCCAACATGAAGCGCTGCTTCTCGCCGCCGGCGCTCCGGGCGTACTTCGCCGAGTTCTTCTCCACCTTCCTCTTTGTGTTCAT[C/T]
GCCGTCGGCTCCACCATCTCCGCCCGTAAGTCATGCGTTTCACTGCAACCTACGTTCCGCATGTCGTGCGAATTGCTCTGCTTTGTTGGTCTCATACGTG

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	97.90%	0.80%	1.27%	0.00%	NA
All Indica	2759	99.40%	0.30%	0.36%	0.00%	NA
All Japonica	1512	94.60%	2.20%	3.24%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.50%	1.20%	1.34%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.00%	0.25%	0.00%	NA
Temperate Japonica	767	90.10%	4.30%	5.61%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	98.80%	0.00%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	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
vg0427576821	G -> A	LOC_Os04g46490.1	synonymous_variant ; p.Ile33Ile; LOW	synonymous_codon	Average:80.392; most accessible tissue: Zhenshan97 flower, score: 87.789	N	N	N	N