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Detailed information for vg0332150873:

Variant ID: vg0332150873 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 32150873
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.02, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

AACACTAAACTCTTCAGCATCTTTCTGGCATGAATGTAAATTGCCATGTATTTTAATCATGTGATTCATGAATATTGGAATTGGCTGTTCTTGCAAGCTT[A/T]
CAATGGAGTACATCTCTGCATGAAACAACAAACAAATATCCCCCTTCCTCGCCAAAATCACCATGAACGTTTTCCTACCAGTAATCTTTACACGAGCAGA

Reverse complement sequence

TCTGCTCGTGTAAAGATTACTGGTAGGAAAACGTTCATGGTGATTTTGGCGAGGAAGGGGGATATTTGTTTGTTGTTTCATGCAGAGATGTACTCCATTG[T/A]
AAGCTTGCAAGAACAGCCAATTCCAATATTCATGAATCACATGATTAAAATACATGGCAATTTACATTCATGCCAGAAAGATGCTGAAGAGTTTAGTGTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.60%	6.40%	0.00%	0.00%	NA
All Indica	2759	99.10%	0.90%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	0.40%	99.60%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.30%	0.70%	0.00%	0.00%	NA
Indica Intermediate	786	97.60%	2.40%	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	93.80%	6.20%	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
vg0332150873	A -> T	LOC_Os03g56400.1	3_prime_UTR_variant ; 75.0bp to feature; MODIFIER	silent_mutation	Average:66.418; most accessible tissue: Zhenshan97 flag leaf, score: 79.247	N	N	N	N
vg0332150873	A -> T	LOC_Os03g56410.1	upstream_gene_variant ; 3036.0bp to feature; MODIFIER	silent_mutation	Average:66.418; most accessible tissue: Zhenshan97 flag leaf, score: 79.247	N	N	N	N
vg0332150873	A -> T	LOC_Os03g56410.2	upstream_gene_variant ; 3008.0bp to feature; MODIFIER	silent_mutation	Average:66.418; most accessible tissue: Zhenshan97 flag leaf, score: 79.247	N	N	N	N
vg0332150873	A -> T	LOC_Os03g56380.1	downstream_gene_variant ; 4206.0bp to feature; MODIFIER	silent_mutation	Average:66.418; most accessible tissue: Zhenshan97 flag leaf, score: 79.247	N	N	N	N
vg0332150873	A -> T	LOC_Os03g56390.1	downstream_gene_variant ; 115.0bp to feature; MODIFIER	silent_mutation	Average:66.418; most accessible tissue: Zhenshan97 flag leaf, score: 79.247	N	N	N	N