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Detailed information for vg0139512311:

Variant ID: vg0139512311 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 39512311
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 363. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGAAACGAATTACAAGCAAATCCACATGCCGACATAGAACATAAGAACTACACCACGTAGCCAGACGTGGCACGACGACGCCTAGGACGTGGTCGAGT[G/A]
GAGGTAGTGCCTTCACCCGTAGGGCGAGCTCCATCTGCTGCTGATCCTGATAGTCCTGCCTCCGCCGCACTTGGTTTCTCCTTGTCTTTAGGACAATGCT

Reverse complement sequence

AGCATTGTCCTAAAGACAAGGAGAAACCAAGTGCGGCGGAGGCAGGACTATCAGGATCAGCAGCAGATGGAGCTCGCCCTACGGGTGAAGGCACTACCTC[C/T]
ACTCGACCACGTCCTAGGCGTCGTCGTGCCACGTCTGGCTACGTGGTGTAGTTCTTATGTTCTATGTCGGCATGTGGATTTGCTTGTAATTCGTTTCGAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.20%	0.20%	10.94%	49.68%	NA
All Indica	2759	21.90%	0.30%	14.53%	63.32%	NA
All Japonica	1512	76.00%	0.10%	4.50%	19.38%	NA
Aus	269	8.60%	0.00%	11.15%	80.30%	NA
Indica I	595	17.80%	0.00%	14.45%	67.73%	NA
Indica II	465	6.20%	0.00%	9.68%	84.09%	NA
Indica III	913	31.50%	0.70%	15.88%	51.92%	NA
Indica Intermediate	786	23.00%	0.10%	15.90%	60.94%	NA
Temperate Japonica	767	97.40%	0.00%	0.65%	1.96%	NA
Tropical Japonica	504	54.80%	0.40%	10.91%	33.93%	NA
Japonica Intermediate	241	52.30%	0.00%	3.32%	44.40%	NA
VI/Aromatic	96	28.10%	0.00%	12.50%	59.38%	NA
Intermediate	90	54.40%	0.00%	6.67%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0139512311	G -> A	LOC_Os01g67990.1	synonymous_variant ; p.Ser861Ser; LOW	synonymous_codon	Average:7.472; most accessible tissue: Callus, score: 21.029	N	N	N	N
vg0139512311	G -> DEL	LOC_Os01g67990.1	N	frameshift_variant	Average:7.472; most accessible tissue: Callus, score: 21.029	N	N	N	N