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Detailed information for vg0727003948:

Variant ID: vg0727003948 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 27003948
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.75, G: 0.26, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

GTGTGACCTGCATGGAAATCAAGGAGAACAAATATTTTCCCGGGGAAGAGGTTCAAAAGTTTAAGGTTCAGTCAAATCAGAAGAAGGTTGTTGTTCAATT[A/G]
ACATCGGAGTATACCCGCATCAGTAGGGATCATGCACGCGAGCTCACGAAACGCGCTGAATGTTCCTGCAACAAGTCAAAGCTGCTTCATAAGCCCTGTT

Reverse complement sequence

AACAGGGCTTATGAAGCAGCTTTGACTTGTTGCAGGAACATTCAGCGCGTTTCGTGAGCTCGCGTGCATGATCCCTACTGATGCGGGTATACTCCGATGT[T/C]
AATTGAACAACAACCTTCTTCTGATTTGACTGAACCTTAAACTTTTGAACCTCTTCCCCGGGAAAATATTTGTTCTCCTTGATTTCCATGCAGGTCACAC

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	98.40%	1.60%	0.06%	0.00%	NA
All Indica	2759	98.90%	0.90%	0.11%	0.00%	NA
All Japonica	1512	97.40%	2.60%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	97.80%	1.50%	0.65%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	98.20%	1.80%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	92.30%	7.70%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0727003948	A -> G	LOC_Os07g45250.1	synonymous_variant ; p.Leu628Leu; LOW	synonymous_codon	Average:61.786; most accessible tissue: Callus, score: 83.754	N	N	N	N