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Detailed information for vg1200352034:

Variant ID: vg1200352034 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 352034
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTATCTAGGATTTATCTGTTCTCTGAAACATGGTTGTTGATATCTAAAATCGTGTGTAGAACTATCAGCTAGGTGGGTCAAGTGCCACATTTTTTGTC[G/A]
TGTTTTTATGTATTCATCTTGATGTATATTACTATTACTTCAAAAATGTTTCCAGACCTATTCTATGTGCTTTATTAGTCAAGTTTTCAGCTGATAATAA

Reverse complement sequence

TTATTATCAGCTGAAAACTTGACTAATAAAGCACATAGAATAGGTCTGGAAACATTTTTGAAGTAATAGTAATATACATCAAGATGAATACATAAAAACA[C/T]
GACAAAAAATGTGGCACTTGACCCACCTAGCTGATAGTTCTACACACGATTTTAGATATCAACAACCATGTTTCAGAGAACAGATAAATCCTAGATAACT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(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	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	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.50%	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	97.90%	2.10%	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
vg1200352034	G -> A	LOC_Os12g01574.1	upstream_gene_variant ; 1389.0bp to feature; MODIFIER	N	Average:59.415; most accessible tissue: Minghui63 flag leaf, score: 81.566	N	N	N	N
vg1200352034	G -> A	LOC_Os12g01570.1	downstream_gene_variant ; 2889.0bp to feature; MODIFIER	N	Average:59.415; most accessible tissue: Minghui63 flag leaf, score: 81.566	N	N	N	N
vg1200352034	G -> A	LOC_Os12g01590.1	downstream_gene_variant ; 3489.0bp to feature; MODIFIER	N	Average:59.415; most accessible tissue: Minghui63 flag leaf, score: 81.566	N	N	N	N
vg1200352034	G -> A	LOC_Os12g01580.1	intron_variant ; MODIFIER	N	Average:59.415; most accessible tissue: Minghui63 flag leaf, score: 81.566	N	N	N	N
vg1200352034	G -> A	LOC_Os12g01580.2	intron_variant ; MODIFIER	N	Average:59.415; most accessible tissue: Minghui63 flag leaf, score: 81.566	N	N	N	N