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Detailed information for vg0222935812:

Variant ID: vg0222935812 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22935812
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 359. )

Flanking Sequence (100 bp) in Reference Genome:

GCAGCAAAGCCCACTACCTTGTCTTGTAAGCCCATCAGTAGAGCATGTATCCAACACATTACTCAATCCAAAGATCAACCACCGATCGGACGCAATCTTC[G/A]
GTGATCAGGTTAATCTAAGAGCAATTAAGTTTTGTCATAGTTGCATGAGTAACAAGTTCTTGTAGGAAGAATAAACTTTGCAGTCTGACTGAGGTCAATG

Reverse complement sequence

CATTGACCTCAGTCAGACTGCAAAGTTTATTCTTCCTACAAGAACTTGTTACTCATGCAACTATGACAAAACTTAATTGCTCTTAGATTAACCTGATCAC[C/T]
GAAGATTGCGTCCGATCGGTGGTTGATCTTTGGATTGAGTAATGTGTTGGATACATGCTCTACTGATGGGCTTACAAGACAAGGTAGTGGGCTTTGCTGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.90%	0.10%	0.02%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	99.50%	0.40%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	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	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	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
vg0222935812	G -> A	LOC_Os02g37950.1	missense_variant ; p.Gly86Ser; MODERATE	N	Average:66.41; most accessible tissue: Minghui63 young leaf, score: 79.191	N	N	N	N
vg0222935812	G -> A	LOC_Os02g37950.2	missense_variant ; p.Gly86Ser; MODERATE	N	Average:66.41; most accessible tissue: Minghui63 young leaf, score: 79.191	N	N	N	N
vg0222935812	G -> A	LOC_Os02g37950.3	missense_variant ; p.Gly86Ser; MODERATE	N	Average:66.41; most accessible tissue: Minghui63 young leaf, score: 79.191	N	N	N	N
vg0222935812	G -> A	LOC_Os02g37940.1	upstream_gene_variant ; 2318.0bp to feature; MODIFIER	N	Average:66.41; most accessible tissue: Minghui63 young leaf, score: 79.191	N	N	N	N
vg0222935812	G -> A	LOC_Os02g37940.2	upstream_gene_variant ; 2267.0bp to feature; MODIFIER	N	Average:66.41; most accessible tissue: Minghui63 young leaf, score: 79.191	N	N	N	N