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Detailed information for vg0302709030:

Variant ID: vg0302709030 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 2709030
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

TCCGGGACAGTATACAAAGGTCAGCTTAATGACGGCACTCTTATCGCCGTCAAACGGGCCAAGAAGGTTTGCTCTTATTTCTTAATGTTCATTTTGCAGA[C/A]
TGCATTAGCTATTGAATACTGATTACCTTGGTCGCCTTTCTTTGCAGAATGTGTACGACAAGCATATGGGTCGTGAGTTCCGGAACGAGATTGAGACGTT

Reverse complement sequence

AACGTCTCAATCTCGTTCCGGAACTCACGACCCATATGCTTGTCGTACACATTCTGCAAAGAAAGGCGACCAAGGTAATCAGTATTCAATAGCTAATGCA[G/T]
TCTGCAAAATGAACATTAAGAAATAAGAGCAAACCTTCTTGGCCCGTTTGACGGCGATAAGAGTGCCGTCATTAAGCTGACCTTTGTATACTGTCCCGGA

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	99.90%	0.10%	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	98.10%	1.90%	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	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
vg0302709030	C -> A	LOC_Os03g05480.1	downstream_gene_variant ; 4283.0bp to feature; MODIFIER	N	Average:70.169; most accessible tissue: Callus, score: 85.954	N	N	N	N
vg0302709030	C -> A	LOC_Os03g05470.1	intron_variant ; MODIFIER	N	Average:70.169; most accessible tissue: Callus, score: 85.954	N	N	N	N