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Detailed information for vg0420225748:

Variant ID: vg0420225748 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 20225748
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

ATATTCATTGAAAACAGCAGCAATCTATGTCAACATTCAATTTCAGCATATTTACAGGATAAAAAATATTCAAAATAGTGAACAAACAATGTGGACTTGA[T/A]
AACTGAACAAAAAATGAACTATTGGAATTTGGAAAGCGCAAAGTTCGCGATATAACTTGATTCAAAAATTAATTTAAGTTTAAGAAACTAAAAGATCAAG

Reverse complement sequence

CTTGATCTTTTAGTTTCTTAAACTTAAATTAATTTTTGAATCAAGTTATATCGCGAACTTTGCGCTTTCCAAATTCCAATAGTTCATTTTTTGTTCAGTT[A/T]
TCAAGTCCACATTGTTTGTTCACTATTTTGAATATTTTTTATCCTGTAAATATGCTGAAATTGAATGTTGACATAGATTGCTGCTGTTTTCAATGAATAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.20%	0.80%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	97.80%	2.20%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	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	95.70%	4.30%	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	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0420225748	T -> A	LOC_Os04g33450.1	upstream_gene_variant ; 2674.0bp to feature; MODIFIER	silent_mutation	Average:63.073; most accessible tissue: Callus, score: 84.585	N	N	N	N
vg0420225748	T -> A	LOC_Os04g33450.3	upstream_gene_variant ; 2674.0bp to feature; MODIFIER	silent_mutation	Average:63.073; most accessible tissue: Callus, score: 84.585	N	N	N	N
vg0420225748	T -> A	LOC_Os04g33450.2	upstream_gene_variant ; 2666.0bp to feature; MODIFIER	silent_mutation	Average:63.073; most accessible tissue: Callus, score: 84.585	N	N	N	N
vg0420225748	T -> A	LOC_Os04g33430.1	downstream_gene_variant ; 1136.0bp to feature; MODIFIER	silent_mutation	Average:63.073; most accessible tissue: Callus, score: 84.585	N	N	N	N
vg0420225748	T -> A	LOC_Os04g33420.1	downstream_gene_variant ; 3474.0bp to feature; MODIFIER	silent_mutation	Average:63.073; most accessible tissue: Callus, score: 84.585	N	N	N	N
vg0420225748	T -> A	LOC_Os04g33440.2	intron_variant ; MODIFIER	silent_mutation	Average:63.073; most accessible tissue: Callus, score: 84.585	N	N	N	N