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Detailed information for vg1223325757:

Variant ID: vg1223325757 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23325757
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

TCGCTAAGGAGATAGCTGGTTGTATTGTGAATACAGAGTGCCTTGCCCACTTGCATTGCATACATCAAGGACCAAGTGGCAAAAGCTATCTTGCACACTA[G/A]
CTAGATACATGAAACATGAGCACACTTGCAATGTTACATAGCTGTAAATATTTAGATCCATGCTAATGATTCTTCTACAAAAGCACTTCACTTCTGCTAG

Reverse complement sequence

CTAGCAGAAGTGAAGTGCTTTTGTAGAAGAATCATTAGCATGGATCTAAATATTTACAGCTATGTAACATTGCAAGTGTGCTCATGTTTCATGTATCTAG[C/T]
TAGTGTGCAAGATAGCTTTTGCCACTTGGTCCTTGATGTATGCAATGCAAGTGGGCAAGGCACTCTGTATTCACAATACAACCAGCTATCTCCTTAGCGA

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	96.60%	3.40%	0.00%	0.00%	NA
All Indica	2759	94.30%	5.70%	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	93.60%	6.40%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	94.60%	5.40%	0.00%	0.00%	NA
Indica Intermediate	786	91.10%	8.90%	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	96.70%	3.30%	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
vg1223325757	G -> A	LOC_Os12g37970.1	3_prime_UTR_variant ; 141.0bp to feature; MODIFIER	silent_mutation	Average:69.578; most accessible tissue: Callus, score: 88.605	N	N	N	N
vg1223325757	G -> A	LOC_Os12g37970.2	3_prime_UTR_variant ; 141.0bp to feature; MODIFIER	silent_mutation	Average:69.578; most accessible tissue: Callus, score: 88.605	N	N	N	N
vg1223325757	G -> A	LOC_Os12g37970.3	3_prime_UTR_variant ; 141.0bp to feature; MODIFIER	silent_mutation	Average:69.578; most accessible tissue: Callus, score: 88.605	N	N	N	N
vg1223325757	G -> A	LOC_Os12g37960.1	downstream_gene_variant ; 2004.0bp to feature; MODIFIER	silent_mutation	Average:69.578; most accessible tissue: Callus, score: 88.605	N	N	N	N
vg1223325757	G -> A	LOC_Os12g37960.2	downstream_gene_variant ; 2004.0bp to feature; MODIFIER	silent_mutation	Average:69.578; most accessible tissue: Callus, score: 88.605	N	N	N	N