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Detailed information for vg0108457605:

Variant ID: vg0108457605 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 8457605
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

CGCCGCCGGATATCGACTTGAAGGATAGGCATGGCTATTCCCCTACGGTGTCTCCGGATACCGTCAGGAGATACGAAAGCGCTATCTCTGATCTCGCCGG[G/A]
CACAGATTCGAGGAGGAAGACTACCCTGTTGTCGACTACGAGTCAGACCTTCAGACCGACATGTCCACAACAGTTAGATAGGCTACCCACATATTGTACT

Reverse complement sequence

AGTACAATATGTGGGTAGCCTATCTAACTGTTGTGGACATGTCGGTCTGAAGGTCTGACTCGTAGTCGACAACAGGGTAGTCTTCCTCCTCGAATCTGTG[C/T]
CCGGCGAGATCAGAGATAGCGCTTTCGTATCTCCTGACGGTATCCGGAGACACCGTAGGGGAATAGCCATGCCTATCCTTCAAGTCGATATCCGGCGGCG

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	99.90%	0.10%	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	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	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	99.90%	0.10%	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	99.00%	1.00%	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
vg0108457605	G -> A	LOC_Os01g15070.1	synonymous_variant ; p.Gly60Gly; LOW	N	Average:54.262; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0108457605	G -> A	LOC_Os01g15080.1	upstream_gene_variant ; 354.0bp to feature; MODIFIER	N	Average:54.262; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0108457605	G -> A	LOC_Os01g15090.1	upstream_gene_variant ; 3467.0bp to feature; MODIFIER	N	Average:54.262; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N
vg0108457605	G -> A	LOC_Os01g15060.1	downstream_gene_variant ; 1583.0bp to feature; MODIFIER	N	Average:54.262; most accessible tissue: Minghui63 young leaf, score: 68.745	N	N	N	N