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Detailed information for vg1013502325:

Variant ID: vg1013502325 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13502325
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.11, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

CAGGTTCCATAGGCATAGTGTTTACTAGCTGCTCTGCTTCGTCTAAATGGCCTGCCCTGCCTAGTAAGTCTATCATACATGAATAATGTTTCATTTTCCT[C/T]
TCAAGATGATATTTTGTCTCCATCAGAGAGAAAAATTCCCGACCTTCTTTCACCAAACCAGCATGACAGCATGCTGAAAGAACACCTATAAACGTAATCT

Reverse complement sequence

AGATTACGTTTATAGGTGTTCTTTCAGCATGCTGTCATGCTGGTTTGGTGAAAGAAGGTCGGGAATTTTTCTCTCTGATGGAGACAAAATATCATCTTGA[G/A]
AGGAAAATGAAACATTATTCATGTATGATAGACTTACTAGGCAGGGCAGGCCATTTAGACGAAGCAGAGCAGCTAGTAAACACTATGCCTATGGAACCTG

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	98.90%	1.10%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	99.40%	0.60%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	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	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	61.50%	38.50%	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
vg1013502325	C -> T	LOC_Os10g26070.1	synonymous_variant ; p.Glu494Glu; LOW	synonymous_codon	Average:52.921; most accessible tissue: Callus, score: 75.764	N	N	N	N