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Detailed information for vg0202003824:

Variant ID: vg0202003824 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2003824
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.89, C: 0.11, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

AGACTGGTCCACTAGCTGACACCTCACAGAGCAAGAAATATTTTGCTCGGATGAACACTAAAGTAGGGTTTTGCAGGGTAAGTGGCAAGTGATGATCCCA[C/A]
TTCACTAAATTACCTGTTTCTGCATTGCTAATCGGAGTGATCAGTTAACTAAATGCTGAAAATATTCTTGTTCTGTTCAGGTGAGAGTGCCGTTCTCAGA

Reverse complement sequence

TCTGAGAACGGCACTCTCACCTGAACAGAACAAGAATATTTTCAGCATTTAGTTAACTGATCACTCCGATTAGCAATGCAGAAACAGGTAATTTAGTGAA[G/T]
TGGGATCATCACTTGCCACTTACCCTGCAAAACCCTACTTTAGTGTTCATCCGAGCAAAATATTTCTTGCTCTGTGAGGTGTCAGCTAGTGGACCAGTCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.70%	3.30%	0.00%	0.00%	NA
All Indica	2759	95.10%	4.90%	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	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	87.70%	12.30%	0.00%	0.00%	NA
Indica Intermediate	786	97.30%	2.70%	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	95.60%	4.40%	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
vg0202003824	C -> A	LOC_Os02g04520.1	upstream_gene_variant ; 3408.0bp to feature; MODIFIER	silent_mutation	Average:70.785; most accessible tissue: Minghui63 flag leaf, score: 89.016	N	N	N	N
vg0202003824	C -> A	LOC_Os02g04520.2	upstream_gene_variant ; 3408.0bp to feature; MODIFIER	silent_mutation	Average:70.785; most accessible tissue: Minghui63 flag leaf, score: 89.016	N	N	N	N
vg0202003824	C -> A	LOC_Os02g04500.1	downstream_gene_variant ; 2903.0bp to feature; MODIFIER	silent_mutation	Average:70.785; most accessible tissue: Minghui63 flag leaf, score: 89.016	N	N	N	N
vg0202003824	C -> A	LOC_Os02g04500.2	downstream_gene_variant ; 2903.0bp to feature; MODIFIER	silent_mutation	Average:70.785; most accessible tissue: Minghui63 flag leaf, score: 89.016	N	N	N	N
vg0202003824	C -> A	LOC_Os02g04510.1	intron_variant ; MODIFIER	silent_mutation	Average:70.785; most accessible tissue: Minghui63 flag leaf, score: 89.016	N	N	N	N