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Detailed information for vg0420225145:

Variant ID: vg0420225145 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 20225145
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, G: 0.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

TCATTCCAGGGTTCAGTCCCTTGTTGACCTCCTCAATGACTACATTGTTCTGAAGACCAGAAAACAAATCTATCAAGCACTATGCATGACAAAAGGGCAC[T/G]
GCAATTTAAATGTATGTGACTTCTTTATCGAAAAAATACTATGAGGCTTGCAGGGTTAGAAGAAGTTAACCCTTCCATAGGAGTATATGTTACAAGTTAC

Reverse complement sequence

GTAACTTGTAACATATACTCCTATGGAAGGGTTAACTTCTTCTAACCCTGCAAGCCTCATAGTATTTTTTCGATAAAGAAGTCACATACATTTAAATTGC[A/C]
GTGCCCTTTTGTCATGCATAGTGCTTGATAGATTTGTTTTCTGGTCTTCAGAACAATGTAGTCATTGAGGAGGTCAACAAGGGACTGAACCCTGGAATGA

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	99.40%	0.60%	0.00%	0.00%	NA
All Indica	2759	99.00%	1.00%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	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	97.30%	2.70%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	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	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
vg0420225145	T -> G	LOC_Os04g33450.1	upstream_gene_variant ; 2071.0bp to feature; MODIFIER	N	Average:67.524; most accessible tissue: Zhenshan97 flower, score: 85.314	N	N	N	N
vg0420225145	T -> G	LOC_Os04g33450.3	upstream_gene_variant ; 2071.0bp to feature; MODIFIER	N	Average:67.524; most accessible tissue: Zhenshan97 flower, score: 85.314	N	N	N	N
vg0420225145	T -> G	LOC_Os04g33450.2	upstream_gene_variant ; 2063.0bp to feature; MODIFIER	N	Average:67.524; most accessible tissue: Zhenshan97 flower, score: 85.314	N	N	N	N
vg0420225145	T -> G	LOC_Os04g33430.1	downstream_gene_variant ; 1739.0bp to feature; MODIFIER	N	Average:67.524; most accessible tissue: Zhenshan97 flower, score: 85.314	N	N	N	N
vg0420225145	T -> G	LOC_Os04g33420.1	downstream_gene_variant ; 4077.0bp to feature; MODIFIER	N	Average:67.524; most accessible tissue: Zhenshan97 flower, score: 85.314	N	N	N	N
vg0420225145	T -> G	LOC_Os04g33440.2	intron_variant ; MODIFIER	N	Average:67.524; most accessible tissue: Zhenshan97 flower, score: 85.314	N	N	N	N