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Detailed information for vg0202002748:

Variant ID: vg0202002748 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2002748
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, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:

CTAATAACAAAACATTACAGAGTCCATCTGTAGACTGCAAGATAATCTTATTAAGGCTAATTAATCCGTCATTAGCAAATGTTTACGGTAACATCACATT[G/A]
TCAAATTATGGCGTAATTAGGCTCAAAAGATTCGTCTTGCAATTTATCTATGTTATTTTTTTTTTGAAACAGGCTCTGGTCAGAAGGAATGATCAAGAAG

Reverse complement sequence

CTTCTTGATCATTCCTTCTGACCAGAGCCTGTTTCAAAAAAAAAATAACATAGATAAATTGCAAGACGAATCTTTTGAGCCTAATTACGCCATAATTTGA[C/T]
AATGTGATGTTACCGTAAACATTTGCTAATGACGGATTAATTAGCCTTAATAAGATTATCTTGCAGTCTACAGATGGACTCTGTAATGTTTTGTTATTAG

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	96.80%	2.90%	0.30%	0.00%	NA
All Indica	2759	94.60%	4.90%	0.51%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.30%	0.00%	0.67%	0.00%	NA
Indica II	465	87.10%	12.00%	0.86%	0.00%	NA
Indica III	913	95.20%	4.70%	0.11%	0.00%	NA
Indica Intermediate	786	94.90%	4.50%	0.64%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	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	96.70%	3.30%	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
vg0202002748	G -> A	LOC_Os02g04520.1	upstream_gene_variant ; 4484.0bp to feature; MODIFIER	silent_mutation	Average:73.118; most accessible tissue: Minghui63 flag leaf, score: 88.103	N	N	N	N
vg0202002748	G -> A	LOC_Os02g04520.2	upstream_gene_variant ; 4484.0bp to feature; MODIFIER	silent_mutation	Average:73.118; most accessible tissue: Minghui63 flag leaf, score: 88.103	N	N	N	N
vg0202002748	G -> A	LOC_Os02g04500.1	downstream_gene_variant ; 1827.0bp to feature; MODIFIER	silent_mutation	Average:73.118; most accessible tissue: Minghui63 flag leaf, score: 88.103	N	N	N	N
vg0202002748	G -> A	LOC_Os02g04500.2	downstream_gene_variant ; 1827.0bp to feature; MODIFIER	silent_mutation	Average:73.118; most accessible tissue: Minghui63 flag leaf, score: 88.103	N	N	N	N
vg0202002748	G -> A	LOC_Os02g04510.1	intron_variant ; MODIFIER	silent_mutation	Average:73.118; most accessible tissue: Minghui63 flag leaf, score: 88.103	N	N	N	N