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Detailed information for vg1223515304:

Variant ID: vg1223515304 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23515304
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

TACGTTCGATCTTCAGCTATTGATTCTGAATATGTTTGCTATGTATTTGTCAACATAAACTGTCATAAGCTTTGATGATTTTGATGTACTTTCCATCATA[G/T]
AAGAATACTATGTTAGCCCCAATAGTTCTGCTTACAATTGATTTGAAGTTATATTCAGTTGAAGCCATCCATAAGACAAAAAAAAAGTTGTCATTTCTAG

Reverse complement sequence

CTAGAAATGACAACTTTTTTTTTGTCTTATGGATGGCTTCAACTGAATATAACTTCAAATCAATTGTAAGCAGAACTATTGGGGCTAACATAGTATTCTT[C/A]
TATGATGGAAAGTACATCAAAATCATCAAAGCTTATGACAGTTTATGTTGACAAATACATAGCAAACATATTCAGAATCAATAGCTGAAGATCGAACGTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.60%	4.40%	0.00%	0.00%	NA
All Indica	2759	92.60%	7.40%	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	77.60%	22.40%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	97.40%	2.60%	0.00%	0.00%	NA
Indica Intermediate	786	94.30%	5.70%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	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	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg1223515304	G -> T	LOC_Os12g38310.1	upstream_gene_variant ; 1348.0bp to feature; MODIFIER	silent_mutation	Average:62.19; most accessible tissue: Minghui63 root, score: 88.578	N	N	N	N
vg1223515304	G -> T	LOC_Os12g38280.1	downstream_gene_variant ; 4723.0bp to feature; MODIFIER	silent_mutation	Average:62.19; most accessible tissue: Minghui63 root, score: 88.578	N	N	N	N
vg1223515304	G -> T	LOC_Os12g38290.1	downstream_gene_variant ; 1827.0bp to feature; MODIFIER	silent_mutation	Average:62.19; most accessible tissue: Minghui63 root, score: 88.578	N	N	N	N
vg1223515304	G -> T	LOC_Os12g38320.1	downstream_gene_variant ; 4664.0bp to feature; MODIFIER	silent_mutation	Average:62.19; most accessible tissue: Minghui63 root, score: 88.578	N	N	N	N
vg1223515304	G -> T	LOC_Os12g38300.1	intron_variant ; MODIFIER	silent_mutation	Average:62.19; most accessible tissue: Minghui63 root, score: 88.578	N	N	N	N