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Detailed information for vg0725680995:

Variant ID: vg0725680995 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 25680995
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

AAATGATCAATATTTCTAAGCAAAAAAAAGATACATTTTTTCTAAAATAAAGCATTAATAAAGCTTTCTAAAATATTGAATTATTGGTGATGATAAATTT[G/T]
TTTTCCATCAAGTGATTATCCAGAATTTGTAGGCCAAATTTTGGAGGTGTTAATTAAATATGATAGTTGATTATCTAGTTTGCCAGAATTTGCATAACTA

Reverse complement sequence

TAGTTATGCAAATTCTGGCAAACTAGATAATCAACTATCATATTTAATTAACACCTCCAAAATTTGGCCTACAAATTCTGGATAATCACTTGATGGAAAA[C/A]
AAATTTATCATCACCAATAATTCAATATTTTAGAAAGCTTTATTAATGCTTTATTTTAGAAAAAATGTATCTTTTTTTTGCTTAGAAATATTGATCATTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.60%	2.40%	0.00%	0.00%	NA
All Indica	2759	99.20%	0.80%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	66.20%	33.80%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	98.90%	1.10%	0.00%	0.00%	NA
Indica Intermediate	786	98.90%	1.10%	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	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
vg0725680995	G -> T	LOC_Os07g42885.1	upstream_gene_variant ; 4250.0bp to feature; MODIFIER	silent_mutation	Average:36.637; most accessible tissue: Minghui63 flower, score: 54.496	N	N	N	N
vg0725680995	G -> T	LOC_Os07g42890.1	downstream_gene_variant ; 1147.0bp to feature; MODIFIER	silent_mutation	Average:36.637; most accessible tissue: Minghui63 flower, score: 54.496	N	N	N	N
vg0725680995	G -> T	LOC_Os07g42900.1	downstream_gene_variant ; 2278.0bp to feature; MODIFIER	silent_mutation	Average:36.637; most accessible tissue: Minghui63 flower, score: 54.496	N	N	N	N
vg0725680995	G -> T	LOC_Os07g42890.2	downstream_gene_variant ; 1192.0bp to feature; MODIFIER	silent_mutation	Average:36.637; most accessible tissue: Minghui63 flower, score: 54.496	N	N	N	N
vg0725680995	G -> T	LOC_Os07g42895.1	intron_variant ; MODIFIER	silent_mutation	Average:36.637; most accessible tissue: Minghui63 flower, score: 54.496	N	N	N	N