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Detailed information for vg0220739690:

Variant ID: vg0220739690 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20739690
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

TCCTGCCATCACGCCAGAAAAAATTAGTCATCCGACCGCCTCGGTCTATTTGAACATCCCAATAGAACATACCATCTTCATTTGCCCTGCTCTTAAGGTG[T/C]
CTTACAAGGTTCTGCAAATCTGCATTCCCTATGGCAAGTGTCCTTGCCATACTAATGTAGCATGAGAGTGAATCTTGCTTTGACGTCTCTACAGAACTTG

Reverse complement sequence

CAAGTTCTGTAGAGACGTCAAAGCAAGATTCACTCTCATGCTACATTAGTATGGCAAGGACACTTGCCATAGGGAATGCAGATTTGCAGAACCTTGTAAG[A/G]
CACCTTAAGAGCAGGGCAAATGAAGATGGTATGTTCTATTGGGATGTTCAAATAGACCGAGGCGGTCGGATGACTAATTTTTTCTGGCGTGATGGCAGGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.10%	21.80%	0.08%	0.00%	NA
All Indica	2759	63.40%	36.40%	0.14%	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	28.90%	70.90%	0.17%	0.00%	NA
Indica II	465	64.90%	34.80%	0.22%	0.00%	NA
Indica III	913	81.30%	18.60%	0.11%	0.00%	NA
Indica Intermediate	786	67.90%	31.90%	0.13%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg0220739690	T -> C	LOC_Os02g34590.1	synonymous_variant ; p.Arg243Arg; LOW	synonymous_codon	Average:65.413; most accessible tissue: Callus, score: 80.956	N	N	N	N