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Detailed information for vg0335315030:

Variant ID: vg0335315030 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 35315030
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.00, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:

CATTTGGAGGCCATGATATATCATATAAAGAGAACGAAAACATAGATTCTGTGTCAACAGCTGAAGTGGATTCACATTCGGAATCACAATTCAACCTTGG[A/G]
CTTGCATCTGATTTAAATGATTTGTTGTCTGCAACTGAAGTATAACGGCTTGGAAGCCTCATTGCCCACTGAACCATGGAAATTTTGGCCCATTCAAAAG

Reverse complement sequence

CTTTTGAATGGGCCAAAATTTCCATGGTTCAGTGGGCAATGAGGCTTCCAAGCCGTTATACTTCAGTTGCAGACAACAAATCATTTAAATCAGATGCAAG[T/C]
CCAAGGTTGAATTGTGATTCCGAATGTGAATCCACTTCAGCTGTTGACACAGAATCTATGTTTTCGTTCTCTTTATATGATATATCATGGCCTCCAAATG

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	96.50%	3.50%	0.00%	0.00%	NA
All Indica	2759	98.80%	1.20%	0.00%	0.00%	NA
All Japonica	1512	98.90%	1.10%	0.00%	0.00%	NA
Aus	269	60.20%	39.80%	0.00%	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	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	96.30%	3.70%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	96.80%	3.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0335315030	A -> G	LOC_Os03g62340.1	synonymous_variant ; p.Ser532Ser; LOW	synonymous_codon	Average:63.372; most accessible tissue: Callus, score: 79.403	N	N	N	N