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Detailed information for vg1223325839:

Variant ID: vg1223325839 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23325839
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:

AAGCTATCTTGCACACTAGCTAGATACATGAAACATGAGCACACTTGCAATGTTACATAGCTGTAAATATTTAGATCCATGCTAATGATTCTTCTACAAA[A/T]
GCACTTCACTTCTGCTAGGTGGATAATTAACTTGGGTAACCTAGTTCAATATATTGCTTCAATAACATGGGCCCACCCCTTTACCATAACCAAATTGTGG

Reverse complement sequence

CCACAATTTGGTTATGGTAAAGGGGTGGGCCCATGTTATTGAAGCAATATATTGAACTAGGTTACCCAAGTTAATTATCCACCTAGCAGAAGTGAAGTGC[T/A]
TTTGTAGAAGAATCATTAGCATGGATCTAAATATTTACAGCTATGTAACATTGCAAGTGTGCTCATGTTTCATGTATCTAGCTAGTGTGCAAGATAGCTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(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	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	97.00%	3.00%	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	100.00%	0.00%	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
vg1223325839	A -> T	LOC_Os12g37970.1	3_prime_UTR_variant ; 59.0bp to feature; MODIFIER	N	Average:72.653; most accessible tissue: Minghui63 root, score: 86.438	N	N	N	N
vg1223325839	A -> T	LOC_Os12g37970.2	3_prime_UTR_variant ; 59.0bp to feature; MODIFIER	N	Average:72.653; most accessible tissue: Minghui63 root, score: 86.438	N	N	N	N
vg1223325839	A -> T	LOC_Os12g37970.3	3_prime_UTR_variant ; 59.0bp to feature; MODIFIER	N	Average:72.653; most accessible tissue: Minghui63 root, score: 86.438	N	N	N	N
vg1223325839	A -> T	LOC_Os12g37960.1	downstream_gene_variant ; 2086.0bp to feature; MODIFIER	N	Average:72.653; most accessible tissue: Minghui63 root, score: 86.438	N	N	N	N
vg1223325839	A -> T	LOC_Os12g37960.2	downstream_gene_variant ; 2086.0bp to feature; MODIFIER	N	Average:72.653; most accessible tissue: Minghui63 root, score: 86.438	N	N	N	N