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Detailed information for vg0825763614:

Variant ID: vg0825763614 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25763614
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

TCCGTGCGTGCATATAGCTCAATCACTATCACAGTAATCATTACTTAGTACATGTTGTTTTGTAATCTTTGCTAGCGAAAGCTAGTGTTTTTTTTTTATG[T/G]
GCACAACTCGGTGTGCCGCCATACATGCATGTGTGATCGACGTATCAGTCTGTACTCTCCCTTTTTTATCTTGCTAGCGAAAGCTAGTATTTTGAGTATT

Reverse complement sequence

AATACTCAAAATACTAGCTTTCGCTAGCAAGATAAAAAAGGGAGAGTACAGACTGATACGTCGATCACACATGCATGTATGGCGGCACACCGAGTTGTGC[A/C]
CATAAAAAAAAAACACTAGCTTTCGCTAGCAAAGATTACAAAACAACATGTACTAAGTAATGATTACTGTGATAGTGATTGAGCTATATGCACGCACGGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.60%	0.40%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	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	100.00%	0.00%	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	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	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
vg0825763614	T -> G	LOC_Os08g40690.1	3_prime_UTR_variant ; 169.0bp to feature; MODIFIER	silent_mutation	Average:67.046; most accessible tissue: Minghui63 panicle, score: 89.949	N	N	N	N
vg0825763614	T -> G	LOC_Os08g40680.1	upstream_gene_variant ; 3665.0bp to feature; MODIFIER	silent_mutation	Average:67.046; most accessible tissue: Minghui63 panicle, score: 89.949	N	N	N	N
vg0825763614	T -> G	LOC_Os08g40700.1	upstream_gene_variant ; 1359.0bp to feature; MODIFIER	silent_mutation	Average:67.046; most accessible tissue: Minghui63 panicle, score: 89.949	N	N	N	N
vg0825763614	T -> G	LOC_Os08g40710.1	downstream_gene_variant ; 3935.0bp to feature; MODIFIER	silent_mutation	Average:67.046; most accessible tissue: Minghui63 panicle, score: 89.949	N	N	N	N