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Detailed information for vg0132054308:

Variant ID: vg0132054308 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 32054308
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

AACAATGTTTTGGCAAATGCATATCGTATCTCAAGAGAAGAAGCTAGGAGACTCAAGCACAACAGGAGAGTGGAGTCAGGCGTGTTCACTCCTAGTCATG[C/T]
CTACAGTAACTTCCAAGATATCATGACTGCATCATTATAGTATAGGCTTGGATTGCTAGGGATGGTTTCCAAATAAATTACAAGAAATAAAAGACTGCAT

Reverse complement sequence

ATGCAGTCTTTTATTTCTTGTAATTTATTTGGAAACCATCCCTAGCAATCCAAGCCTATACTATAATGATGCAGTCATGATATCTTGGAAGTTACTGTAG[G/A]
CATGACTAGGAGTGAACACGCCTGACTCCACTCTCCTGTTGTGCTTGAGTCTCCTAGCTTCTTCTCTTGAGATACGATATGCATTTGCCAAAACATTGTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(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	99.60%	0.40%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	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
vg0132054308	C -> T	LOC_Os01g55630.1	missense_variant ; p.Ala224Val; MODERATE	N	Average:42.72; most accessible tissue: Callus, score: 84.057	N	N	N	N
vg0132054308	C -> T	LOC_Os01g55620.1	upstream_gene_variant ; 3542.0bp to feature; MODIFIER	N	Average:42.72; most accessible tissue: Callus, score: 84.057	N	N	N	N
vg0132054308	C -> T	LOC_Os01g55640.1	upstream_gene_variant ; 2847.0bp to feature; MODIFIER	N	Average:42.72; most accessible tissue: Callus, score: 84.057	N	N	N	N
vg0132054308	C -> T	LOC_Os01g55650.1	downstream_gene_variant ; 3075.0bp to feature; MODIFIER	N	Average:42.72; most accessible tissue: Callus, score: 84.057	N	N	N	N