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Detailed information for vg0704183416:

Variant ID: vg0704183416 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 4183416
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

ATATCTATACAAGACAGCACATAAAATGTTTTATATTTATTTTAATAAATCCTGCATCTTCTTATAGCCAAATTATAAGAATGATTCTGTGTTGCTATAT[G/T]
TCCTATTAAACACGACAGAATAAACCTTCATGGGTTGCTCATGGGAAACACAATTGAGAAAATACCGTAAACTGCAATGCAAAGAGGACATTAGAGAATC

Reverse complement sequence

GATTCTCTAATGTCCTCTTTGCATTGCAGTTTACGGTATTTTCTCAATTGTGTTTCCCATGAGCAACCCATGAAGGTTTATTCTGTCGTGTTTAATAGGA[C/A]
ATATAGCAACACAGAATCATTCTTATAATTTGGCTATAAGAAGATGCAGGATTTATTAAAATAAATATAAAACATTTTATGTGCTGTCTTGTATAGATAT

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	99.70%	0.30%	0.02%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	99.10%	0.80%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	97.40%	2.40%	0.20%	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	100.00%	0.00%	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
vg0704183416	G -> T	LOC_Os07g08190.1	downstream_gene_variant ; 1767.0bp to feature; MODIFIER	N	Average:64.661; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N
vg0704183416	G -> T	LOC_Os07g08210.1	downstream_gene_variant ; 1789.0bp to feature; MODIFIER	N	Average:64.661; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N
vg0704183416	G -> T	LOC_Os07g08210.3	downstream_gene_variant ; 1789.0bp to feature; MODIFIER	N	Average:64.661; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N
vg0704183416	G -> T	LOC_Os07g08210.2	downstream_gene_variant ; 1789.0bp to feature; MODIFIER	N	Average:64.661; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N
vg0704183416	G -> T	LOC_Os07g08200.1	intron_variant ; MODIFIER	N	Average:64.661; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N