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Detailed information for vg0429945986:

Variant ID: vg0429945986 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 29945986
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: 304. )

Flanking Sequence (100 bp) in Reference Genome:

TGAATAGAGAAGGAGAACTTTACAAAGCGAAAGGACAAAAAGAAAGGAGCTAGGACCTTTGGTCCGAGCTAACTAAAAGAAAGCCAGCTATTAAGACTTC[T/A]
CGCTCCTGCTAAGGCCCAAGTTTTGGCCTCTTCCTTGATCTTGGCTAAAAGAGAGATAGCTGAAAGCTCCTTCTGTTGGAAGGTTCTGCGATTCCTTTCG

Reverse complement sequence

CGAAAGGAATCGCAGAACCTTCCAACAGAAGGAGCTTTCAGCTATCTCTCTTTTAGCCAAGATCAAGGAAGAGGCCAAAACTTGGGCCTTAGCAGGAGCG[A/T]
GAAGTCTTAATAGCTGGCTTTCTTTTAGTTAGCTCGGACCAAAGGTCCTAGCTCCTTTCTTTTTGTCCTTTCGCTTTGTAAAGTTCTCCTTCTCTATTCA

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	94.10%	5.90%	0.00%	0.00%	NA
All Indica	2759	99.30%	0.70%	0.00%	0.00%	NA
All Japonica	1512	83.30%	16.70%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.00%	1.00%	0.00%	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	99.00%	1.00%	0.00%	0.00%	NA
Temperate Japonica	767	92.40%	7.60%	0.00%	0.00%	NA
Tropical Japonica	504	92.90%	7.10%	0.00%	0.00%	NA
Japonica Intermediate	241	34.40%	65.60%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0429945986	T -> A	LOC_Os04g50188.1	stop_gained ; p.Arg102*; HIGH	stop_gained	Average:49.994; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N