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Detailed information for vg1200522479:

Variant ID: vg1200522479 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 522479
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

CGAAGGCGAGCCAGACGAGCAGAGCCGCGTTCATTGGGTGCTTGGCCCACGCGAGGCACTTGGCGCGGAGGGCGCGCCAGTCGACGGAGCGGACGAACGC[C/T]
GGTAAGCGGCGGGAAGCTGCAGGGTTGTTTGTGGTGCGGAGGGAGGCGAGGCGGGTGAGGAAGGCGGCGCCGGAGAAGGAGAACCATGGTGTCTTGGACG

Reverse complement sequence

CGTCCAAGACACCATGGTTCTCCTTCTCCGGCGCCGCCTTCCTCACCCGCCTCGCCTCCCTCCGCACCACAAACAACCCTGCAGCTTCCCGCCGCTTACC[G/A]
GCGTTCGTCCGCTCCGTCGACTGGCGCGCCCTCCGCGCCAAGTGCCTCGCGTGGGCCAAGCACCCAATGAACGCGGCTCTGCTCGTCTGGCTCGCCTTCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.00%	4.80%	0.11%	0.00%	NA
All Indica	2759	91.70%	8.10%	0.18%	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	87.60%	11.90%	0.50%	0.00%	NA
Indica II	465	96.30%	3.70%	0.00%	0.00%	NA
Indica III	913	91.00%	8.90%	0.11%	0.00%	NA
Indica Intermediate	786	92.90%	7.00%	0.13%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	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	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg1200522479	C -> T	LOC_Os12g01890.1	synonymous_variant ; p.Pro68Pro; LOW	synonymous_codon	Average:76.614; most accessible tissue: Zhenshan97 root, score: 83.907	N	N	N	N