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Detailed information for vg0202002759:

Variant ID: vg0202002759 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2002759
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, A: 0.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

ACATTACAGAGTCCATCTGTAGACTGCAAGATAATCTTATTAAGGCTAATTAATCCGTCATTAGCAAATGTTTACGGTAACATCACATTGTCAAATTATG[G/A]
CGTAATTAGGCTCAAAAGATTCGTCTTGCAATTTATCTATGTTATTTTTTTTTTGAAACAGGCTCTGGTCAGAAGGAATGATCAAGAAGTGATCGACATG

Reverse complement sequence

CATGTCGATCACTTCTTGATCATTCCTTCTGACCAGAGCCTGTTTCAAAAAAAAAATAACATAGATAAATTGCAAGACGAATCTTTTGAGCCTAATTACG[C/T]
CATAATTTGACAATGTGATGTTACCGTAAACATTTGCTAATGACGGATTAATTAGCCTTAATAAGATTATCTTGCAGTCTACAGATGGACTCTGTAATGT

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	99.70%	0.30%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	94.40%	5.60%	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	99.90%	0.10%	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	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	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
vg0202002759	G -> A	LOC_Os02g04520.1	upstream_gene_variant ; 4473.0bp to feature; MODIFIER	silent_mutation	Average:73.266; most accessible tissue: Minghui63 flag leaf, score: 88.459	N	N	N	N
vg0202002759	G -> A	LOC_Os02g04520.2	upstream_gene_variant ; 4473.0bp to feature; MODIFIER	silent_mutation	Average:73.266; most accessible tissue: Minghui63 flag leaf, score: 88.459	N	N	N	N
vg0202002759	G -> A	LOC_Os02g04500.1	downstream_gene_variant ; 1838.0bp to feature; MODIFIER	silent_mutation	Average:73.266; most accessible tissue: Minghui63 flag leaf, score: 88.459	N	N	N	N
vg0202002759	G -> A	LOC_Os02g04500.2	downstream_gene_variant ; 1838.0bp to feature; MODIFIER	silent_mutation	Average:73.266; most accessible tissue: Minghui63 flag leaf, score: 88.459	N	N	N	N
vg0202002759	G -> A	LOC_Os02g04510.1	intron_variant ; MODIFIER	silent_mutation	Average:73.266; most accessible tissue: Minghui63 flag leaf, score: 88.459	N	N	N	N