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Detailed information for vg0138753354:

Variant ID: vg0138753354 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 38753354
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

TAGGATTTGTATTCTGAAAAACAGCACAAATCATGAATGAGAACACAAGGCGCATGATAATTTTTCACAAGAAAGGCTTGTGTGCCATTTGTGTGGTTCC[G/A]
GGAAATATAGTGTGTTTTACTCTTGGTAGTTCTAGTGAATTGACAATGGTGTGATGTAACTAGTTTTTGGCTAGGGAAAAGTGAAGTGCTTCTATTTCAT

Reverse complement sequence

ATGAAATAGAAGCACTTCACTTTTCCCTAGCCAAAAACTAGTTACATCACACCATTGTCAATTCACTAGAACTACCAAGAGTAAAACACACTATATTTCC[C/T]
GGAACCACACAAATGGCACACAAGCCTTTCTTGTGAAAAATTATCATGCGCCTTGTGTTCTCATTCATGATTTGTGCTGTTTTTCAGAATACAAATCCTA

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	98.00%	2.00%	0.00%	0.00%	NA
All Indica	2759	99.60%	0.40%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	74.30%	25.70%	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	99.30%	0.70%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.60%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0138753354	G -> A	LOC_Os01g66710.1	downstream_gene_variant ; 2586.0bp to feature; MODIFIER	silent_mutation	Average:50.552; most accessible tissue: Zhenshan97 flower, score: 62.865	N	N	N	N
vg0138753354	G -> A	LOC_Os01g66730.1	downstream_gene_variant ; 1704.0bp to feature; MODIFIER	silent_mutation	Average:50.552; most accessible tissue: Zhenshan97 flower, score: 62.865	N	N	N	N
vg0138753354	G -> A	LOC_Os01g66730.2	downstream_gene_variant ; 1732.0bp to feature; MODIFIER	silent_mutation	Average:50.552; most accessible tissue: Zhenshan97 flower, score: 62.865	N	N	N	N
vg0138753354	G -> A	LOC_Os01g66720.1	intron_variant ; MODIFIER	silent_mutation	Average:50.552; most accessible tissue: Zhenshan97 flower, score: 62.865	N	N	N	N