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Detailed information for vg0222935310:

Variant ID: vg0222935310 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22935310
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

AAGTTCAATCGATGTAGGCTCGTCTGGGACACTCGAAATGAAATGATTTTGCAGAATTCATTTTGAAAATTCTCTTTTCGAAGCGAGTCATAAAGAGGAA[T/A]
ATGCATGTTTTCCCCCCTTTTCTCCCTCTTTTTTCGTGATCAGGTTAGTGGAGAGACCCCCCTCTGCATTGTTCAAGACTTCAGACTCGCTACTAAAGTG

Reverse complement sequence

CACTTTAGTAGCGAGTCTGAAGTCTTGAACAATGCAGAGGGGGGTCTCTCCACTAACCTGATCACGAAAAAAGAGGGAGAAAAGGGGGGAAAACATGCAT[A/T]
TTCCTCTTTATGACTCGCTTCGAAAAGAGAATTTTCAAAATGAATTCTGCAAAATCATTTCATTTCGAGTGTCCCAGACGAGCCTACATCGATTGAACTT

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	96.50%	3.50%	0.00%	0.00%	NA
All Indica	2759	98.70%	1.30%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	52.80%	47.20%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	99.10%	0.90%	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	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	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
vg0222935310	T -> A	LOC_Os02g37950.1	5_prime_UTR_variant ; 247.0bp to feature; MODIFIER	silent_mutation	Average:72.853; most accessible tissue: Minghui63 flag leaf, score: 82.289	N	N	N	N
vg0222935310	T -> A	LOC_Os02g37950.3	5_prime_UTR_variant ; 247.0bp to feature; MODIFIER	silent_mutation	Average:72.853; most accessible tissue: Minghui63 flag leaf, score: 82.289	N	N	N	N
vg0222935310	T -> A	LOC_Os02g37940.1	upstream_gene_variant ; 1816.0bp to feature; MODIFIER	silent_mutation	Average:72.853; most accessible tissue: Minghui63 flag leaf, score: 82.289	N	N	N	N
vg0222935310	T -> A	LOC_Os02g37940.2	upstream_gene_variant ; 1765.0bp to feature; MODIFIER	silent_mutation	Average:72.853; most accessible tissue: Minghui63 flag leaf, score: 82.289	N	N	N	N
vg0222935310	T -> A	LOC_Os02g37930.1	downstream_gene_variant ; 4832.0bp to feature; MODIFIER	silent_mutation	Average:72.853; most accessible tissue: Minghui63 flag leaf, score: 82.289	N	N	N	N
vg0222935310	T -> A	LOC_Os02g37950.2	intron_variant ; MODIFIER	silent_mutation	Average:72.853; most accessible tissue: Minghui63 flag leaf, score: 82.289	N	N	N	N