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Detailed information for vg1200762105:

Variant ID: vg1200762105 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 762105
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGCAACAATGAGATATTTCTCGAGATATGAAACATTTTCCCATAAAATAACTAACTTTCTATATATGTGCATTTTTTTCTTTGGTGCAGGGTCAGTTA[A/G]
ATCAATCCTGCTTGGATCGATCGATCGAGCTTAACATGCTAGCTCAATCGGAGTTGATCAGCTAGTAATTAAGCACGTACTTGCTACAGCATATATGAAC

Reverse complement sequence

GTTCATATATGCTGTAGCAAGTACGTGCTTAATTACTAGCTGATCAACTCCGATTGAGCTAGCATGTTAAGCTCGATCGATCGATCCAAGCAGGATTGAT[T/C]
TAACTGACCCTGCACCAAAGAAAAAAATGCACATATATAGAAAGTTAGTTATTTTATGGGAAAATGTTTCATATCTCGAGAAATATCTCATTGTTGCTTT

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%	0.02%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	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	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	1.11%	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
vg1200762105	A -> G	LOC_Os12g02340.2	missense_variant ; p.Asn61Asp; MODERATE	N	Average:41.081; most accessible tissue: Zhenshan97 flower, score: 80.613	N	N	N	N
vg1200762105	A -> G	LOC_Os12g02340.1	stop_retained_variant ; p.Ter119Ter; LOW	N	Average:41.081; most accessible tissue: Zhenshan97 flower, score: 80.613	N	N	N	N
vg1200762105	A -> G	LOC_Os12g02350.1	upstream_gene_variant ; 1686.0bp to feature; MODIFIER	N	Average:41.081; most accessible tissue: Zhenshan97 flower, score: 80.613	N	N	N	N
vg1200762105	A -> G	LOC_Os12g02370.2	downstream_gene_variant ; 4329.0bp to feature; MODIFIER	N	Average:41.081; most accessible tissue: Zhenshan97 flower, score: 80.613	N	N	N	N
vg1200762105	A -> G	LOC_Os12g02370.4	downstream_gene_variant ; 4329.0bp to feature; MODIFIER	N	Average:41.081; most accessible tissue: Zhenshan97 flower, score: 80.613	N	N	N	N