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Detailed information for vg1223326820:

Variant ID: vg1223326820 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23326820
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, A: 0.07, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

AACCTGATACTTTGGCAATGAAATCCCAACGACGTTCACCGAACAATCGGACAGTGCATACCAGTTGCAGGTCCTCCTGCTCTGTCCATGGCCCTTTGCG[T/A]
ATCTCTTCTCTCACTGTCACCATATTGATTACCCTAGTATATGATGACAGTGTTGCACTAACGCTGCTCGCTCCTACCTTGTATCGGCTCGGAGCCGGTC

Reverse complement sequence

GACCGGCTCCGAGCCGATACAAGGTAGGAGCGAGCAGCGTTAGTGCAACACTGTCATCATATACTAGGGTAATCAATATGGTGACAGTGAGAGAAGAGAT[A/T]
CGCAAAGGGCCATGGACAGAGCAGGAGGACCTGCAACTGGTATGCACTGTCCGATTGTTCGGTGAACGTCGTTGGGATTTCATTGCCAAAGTATCAGGTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.50%	7.50%	0.00%	0.00%	NA
All Indica	2759	94.50%	5.50%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	30.90%	69.10%	0.00%	0.00%	NA
Indica I	595	85.20%	14.80%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	98.60%	1.40%	0.00%	0.00%	NA
Indica Intermediate	786	93.80%	6.20%	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	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg1223326820	T -> A	LOC_Os12g37970.1	synonymous_variant ; p.Ile8Ile; LOW	nonsynonymous_codon ; I8T	Average:80.741; most accessible tissue: Zhenshan97 panicle, score: 86.058	unknown	unknown	TOLERATED	0.49