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Detailed information for vg0221474956:

Variant ID: vg0221474956 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21474956
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

ACTACTATTAATTCCAAAGTTCTATACAAATATAAGAAAAAGAGGCAGCCATGGAAGTTCTTGGGAATGCATCATGCAATCCTTGGTTCTATGCAAGCTT[T/A]
TGAAGGACCTTAAAATTACACCATGACACGACAAAGAATAACTTAATTCATTACACCAGTTAGCAAAATACCCCCTCTATATGTAATATACCCTGTGGTA

Reverse complement sequence

TACCACAGGGTATATTACATATAGAGGGGGTATTTTGCTAACTGGTGTAATGAATTAAGTTATTCTTTGTCGTGTCATGGTGTAATTTTAAGGTCCTTCA[A/T]
AAGCTTGCATAGAACCAAGGATTGCATGATGCATTCCCAAGAACTTCCATGGCTGCCTCTTTTTCTTATATTTGTATAGAACTTTGGAATTAATAGTAGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.80%	0.10%	0.02%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.04%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	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
vg0221474956	T -> A	LOC_Os02g35760.1	3_prime_UTR_variant ; 267.0bp to feature; MODIFIER	N	Average:54.343; most accessible tissue: Callus, score: 84.947	N	N	N	N
vg0221474956	T -> A	LOC_Os02g35750.2	3_prime_UTR_variant ; 1535.0bp to feature; MODIFIER	N	Average:54.343; most accessible tissue: Callus, score: 84.947	N	N	N	N
vg0221474956	T -> A	LOC_Os02g35760.2	3_prime_UTR_variant ; 267.0bp to feature; MODIFIER	N	Average:54.343; most accessible tissue: Callus, score: 84.947	N	N	N	N
vg0221474956	T -> A	LOC_Os02g35740.1	upstream_gene_variant ; 3820.0bp to feature; MODIFIER	N	Average:54.343; most accessible tissue: Callus, score: 84.947	N	N	N	N
vg0221474956	T -> A	LOC_Os02g35750.1	downstream_gene_variant ; 1134.0bp to feature; MODIFIER	N	Average:54.343; most accessible tissue: Callus, score: 84.947	N	N	N	N
vg0221474956	T -> A	LOC_Os02g35750.3	intron_variant ; MODIFIER	N	Average:54.343; most accessible tissue: Callus, score: 84.947	N	N	N	N