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Detailed information for vg0725681160:

Variant ID: vg0725681160 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 25681160
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTGATTATCTAGTTTGCCAGAATTTGCATAACTAAGATAGTACATACAGGAAACTGACGTAATTTGCATCAACTTTGCTGATAAACTATCAGATTTAG[A/G]
AAAAAAAAACAAAAGAACACAAGAAATTTACTAACCATGGAATCATCAATAACCAGATCCTTCATTTGGACATCCATAAGCTTCCACAATCCATTGAATC

Reverse complement sequence

GATTCAATGGATTGTGGAAGCTTATGGATGTCCAAATGAAGGATCTGGTTATTGATGATTCCATGGTTAGTAAATTTCTTGTGTTCTTTTGTTTTTTTTT[T/C]
CTAAATCTGATAGTTTATCAGCAAAGTTGATGCAAATTACGTCAGTTTCCTGTATGTACTATCTTAGTTATGCAAATTCTGGCAAACTAGATAATCAACT

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	97.80%	0.20%	1.74%	0.19%	NA
All Indica	2759	99.50%	0.00%	0.51%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	67.70%	3.70%	25.28%	3.35%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	99.20%	0.00%	0.77%	0.00%	NA
Indica Intermediate	786	99.40%	0.00%	0.64%	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	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	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
vg0725681160	A -> DEL	N	N	silent_mutation	Average:41.393; most accessible tissue: Minghui63 flower, score: 62.973	N	N	N	N
vg0725681160	A -> G	LOC_Os07g42885.1	upstream_gene_variant ; 4415.0bp to feature; MODIFIER	silent_mutation	Average:41.393; most accessible tissue: Minghui63 flower, score: 62.973	N	N	N	N
vg0725681160	A -> G	LOC_Os07g42890.1	downstream_gene_variant ; 1312.0bp to feature; MODIFIER	silent_mutation	Average:41.393; most accessible tissue: Minghui63 flower, score: 62.973	N	N	N	N
vg0725681160	A -> G	LOC_Os07g42900.1	downstream_gene_variant ; 2113.0bp to feature; MODIFIER	silent_mutation	Average:41.393; most accessible tissue: Minghui63 flower, score: 62.973	N	N	N	N
vg0725681160	A -> G	LOC_Os07g42890.2	downstream_gene_variant ; 1357.0bp to feature; MODIFIER	silent_mutation	Average:41.393; most accessible tissue: Minghui63 flower, score: 62.973	N	N	N	N
vg0725681160	A -> G	LOC_Os07g42895.1	intron_variant ; MODIFIER	silent_mutation	Average:41.393; most accessible tissue: Minghui63 flower, score: 62.973	N	N	N	N