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Detailed information for vg0427735043:

Variant ID: vg0427735043 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 27735043
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

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

Flanking Sequence (100 bp) in Reference Genome:

TGAATAGCAGCATTGGTTAATCAATGAGGATATGGGATGCATTGGCGTTTGGTGATAGATAGGTGATCTTTTAATGAGCCCTAGTCCTTTAGTTTCCATG[A/G]
AGGGAACATTTGCGTTACTGAGCTACAGTAGTCGACAAACTGGAGTAGGAATAATGCTATTCCTGTTTGTATCTTCTCATCTGAAATAATGATGCACCGG

Reverse complement sequence

CCGGTGCATCATTATTTCAGATGAGAAGATACAAACAGGAATAGCATTATTCCTACTCCAGTTTGTCGACTACTGTAGCTCAGTAACGCAAATGTTCCCT[T/C]
CATGGAAACTAAAGGACTAGGGCTCATTAAAAGATCACCTATCTATCACCAAACGCCAATGCATCCCATATCCTCATTGATTAACCAATGCTGCTATTCA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.60%	0.20%	0.15%	0.00%	NA
All Indica	2759	99.40%	0.40%	0.25%	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	99.20%	0.00%	0.84%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.30%	0.13%	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
vg0427735043	A -> G	LOC_Os04g46800.1	upstream_gene_variant ; 3181.0bp to feature; MODIFIER	N	Average:46.627; most accessible tissue: Callus, score: 87.686	N	N	N	N
vg0427735043	A -> G	LOC_Os04g46770.1	downstream_gene_variant ; 3990.0bp to feature; MODIFIER	N	Average:46.627; most accessible tissue: Callus, score: 87.686	N	N	N	N
vg0427735043	A -> G	LOC_Os04g46790.1	downstream_gene_variant ; 1438.0bp to feature; MODIFIER	N	Average:46.627; most accessible tissue: Callus, score: 87.686	N	N	N	N
vg0427735043	A -> G	LOC_Os04g46780.1	intron_variant ; MODIFIER	N	Average:46.627; most accessible tissue: Callus, score: 87.686	N	N	N	N
vg0427735043	A -> G	LOC_Os04g46780.2	intron_variant ; MODIFIER	N	Average:46.627; most accessible tissue: Callus, score: 87.686	N	N	N	N