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Detailed information for vg0724211942:

Variant ID: vg0724211942 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24211942
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, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

GGCTCGCCACGTTCATGGGGGTCAGCTTCATGTGCCTCTCATTCGTGACGGTGGGCATGGTTCACCTTGTGCTTGTTCTTCATCTTACGATGGTGAGGGG[A/G]
GTCGGCGGTTTTCCAAGGCTGACGATTCTCTTTCGTTGGTTCATGCCTGCTTGCCTCCTGGCGTCCACCTTTGTATACTTTGTCCAGTCCATGCACACAA

Reverse complement sequence

TTGTGTGCATGGACTGGACAAAGTATACAAAGGTGGACGCCAGGAGGCAAGCAGGCATGAACCAACGAAAGAGAATCGTCAGCCTTGGAAAACCGCCGAC[T/C]
CCCCTCACCATCGTAAGATGAAGAACAAGCACAAGGTGAACCATGCCCACCGTCACGAATGAGAGGCACATGAAGCTGACCCCCATGAACGTGGCGAGCC

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	98.10%	1.50%	0.34%	0.00%	NA
All Indica	2759	98.30%	1.70%	0.00%	0.00%	NA
All Japonica	1512	97.20%	1.70%	1.06%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.00%	1.00%	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	95.00%	5.00%	0.00%	0.00%	NA
Temperate Japonica	767	98.60%	0.30%	1.17%	0.00%	NA
Tropical Japonica	504	98.20%	1.60%	0.20%	0.00%	NA
Japonica Intermediate	241	90.90%	6.60%	2.49%	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
vg0724211942	A -> G	LOC_Os07g40380.1	synonymous_variant ; p.Gly101Gly; LOW	synonymous_codon	Average:67.089; most accessible tissue: Callus, score: 97.192	N	N	N	N