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Detailed information for vg0420225386:

Variant ID: vg0420225386 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 20225386
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

ATGAGTCTGCACATATTGCCATGTATAGATCTCCATACACAGATAATTCGAAAGCTAGATAACAATTATTTGTACTGTATAGTCACCCACATCTGTAGTT[C/A]
TGTACAGTTTGATCACAGCACAAAATAAAGCTTATTACTAAGGATTGCATGTTTTCAACACTAGCAACTAGCCCATCCAAGAGTGGCCAAAACTAAATGG

Reverse complement sequence

CCATTTAGTTTTGGCCACTCTTGGATGGGCTAGTTGCTAGTGTTGAAAACATGCAATCCTTAGTAATAAGCTTTATTTTGTGCTGTGATCAAACTGTACA[G/T]
AACTACAGATGTGGGTGACTATACAGTACAAATAATTGTTATCTAGCTTTCGAATTATCTGTGTATGGAGATCTATACATGGCAATATGTGCAGACTCAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.50%	0.50%	0.00%	0.00%	NA
All Indica	2759	99.20%	0.80%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	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	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	98.60%	1.40%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.60%	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
vg0420225386	C -> A	LOC_Os04g33450.1	upstream_gene_variant ; 2312.0bp to feature; MODIFIER	N	Average:64.519; most accessible tissue: Zhenshan97 flower, score: 84.217	N	N	N	N
vg0420225386	C -> A	LOC_Os04g33450.3	upstream_gene_variant ; 2312.0bp to feature; MODIFIER	N	Average:64.519; most accessible tissue: Zhenshan97 flower, score: 84.217	N	N	N	N
vg0420225386	C -> A	LOC_Os04g33450.2	upstream_gene_variant ; 2304.0bp to feature; MODIFIER	N	Average:64.519; most accessible tissue: Zhenshan97 flower, score: 84.217	N	N	N	N
vg0420225386	C -> A	LOC_Os04g33430.1	downstream_gene_variant ; 1498.0bp to feature; MODIFIER	N	Average:64.519; most accessible tissue: Zhenshan97 flower, score: 84.217	N	N	N	N
vg0420225386	C -> A	LOC_Os04g33420.1	downstream_gene_variant ; 3836.0bp to feature; MODIFIER	N	Average:64.519; most accessible tissue: Zhenshan97 flower, score: 84.217	N	N	N	N
vg0420225386	C -> A	LOC_Os04g33440.2	intron_variant ; MODIFIER	N	Average:64.519; most accessible tissue: Zhenshan97 flower, score: 84.217	N	N	N	N