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Detailed information for vg0612160207:

Variant ID: vg0612160207 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 12160207
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

GGCGATTGTCGGCATAACTCTTATGTCGAGACTGAGCCACTCGCAATCTTTATTGAATGATCTTTACCTTTTCTTCTGCTTCCCTTAGGATATCCGTCCC[A/G]
AAAACCTGACGTTCTCCCGTTTGATCCCACAAAAGCGGAGTGCGGCACTTTCGACCATACAGTGCTTCGTAAGGAGCCATCTGTAAACTAGTTTGATAAC

Reverse complement sequence

GTTATCAAACTAGTTTACAGATGGCTCCTTACGAAGCACTGTATGGTCGAAAGTGCCGCACTCCGCTTTTGTGGGATCAAACGGGAGAACGTCAGGTTTT[T/C]
GGGACGGATATCCTAAGGGAAGCAGAAGAAAAGGTAAAGATCATTCAATAAAGATTGCGAGTGGCTCAGTCTCGACATAAGAGTTATGCCGACAATCGCC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.80%	10.10%	49.83%	1.27%	NA
All Indica	2759	14.10%	14.00%	70.28%	1.56%	NA
All Japonica	1512	88.70%	0.50%	9.85%	0.99%	NA
Aus	269	15.20%	30.50%	54.28%	0.00%	NA
Indica I	595	16.50%	6.20%	74.45%	2.86%	NA
Indica II	465	12.70%	11.20%	73.55%	2.58%	NA
Indica III	913	13.50%	22.00%	63.75%	0.77%	NA
Indica Intermediate	786	14.00%	12.30%	72.77%	0.89%	NA
Temperate Japonica	767	97.30%	0.30%	2.09%	0.39%	NA
Tropical Japonica	504	74.40%	0.80%	22.82%	1.98%	NA
Japonica Intermediate	241	91.30%	0.40%	7.47%	0.83%	NA
VI/Aromatic	96	22.90%	0.00%	77.08%	0.00%	NA
Intermediate	90	42.20%	3.30%	52.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0612160207	A -> G	LOC_Os06g21050.1	synonymous_variant ; p.Phe1227Phe; LOW	synonymous_codon	Average:4.878; most accessible tissue: Callus, score: 8.991	N	N	N	N
vg0612160207	A -> DEL	LOC_Os06g21050.1	N	frameshift_variant	Average:4.878; most accessible tissue: Callus, score: 8.991	N	N	N	N