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Detailed information for vg1202836274:

Variant ID: vg1202836274 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 2836274
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

CGACGGCGGCGGCGCCGACGCCGCGCTGCTGCTCTTGGCGTCTGCTTCTCTCTGCGACTCTCCTGCAAATTGTTCCACCGCGAAAGGTATATGATCTTTA[A/G]
TCACTTGCTGTAGTTGCATGTTAATTATAGTATCAAAGTGCTTAATTAATTTGTTCTTGAGTTTCTACTACTAGATATGCAATTGCGTGTTTAGTTAGTT

Reverse complement sequence

AACTAACTAAACACGCAATTGCATATCTAGTAGTAGAAACTCAAGAACAAATTAATTAAGCACTTTGATACTATAATTAACATGCAACTACAGCAAGTGA[T/C]
TAAAGATCATATACCTTTCGCGGTGGAACAATTTGCAGGAGAGTCGCAGAGAGAAGCAGACGCCAAGAGCAGCAGCGCGGCGTCGGCGCCGCCGCCGTCG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.80%	0.20%	0.00%	0.00%	NA
All Indica	2759	99.80%	0.20%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	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	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
vg1202836274	A -> G	LOC_Os12g06070.1	downstream_gene_variant ; 4338.0bp to feature; MODIFIER	N	Average:77.228; most accessible tissue: Zhenshan97 flower, score: 85.807	N	N	N	N
vg1202836274	A -> G	LOC_Os12g06080.1	intron_variant ; MODIFIER	N	Average:77.228; most accessible tissue: Zhenshan97 flower, score: 85.807	N	N	N	N