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Detailed information for vg0703433196:

Variant ID: vg0703433196 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 3433196
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

TAGAACAAATTAATTGTTTTTCAGTTACATCTGATGCTCTGAATAATAATATGATTATATAGCCGCATGCTTCAACTATAATCCTGTATTCTTGTGTACA[C/A]
AAAATGATTCAGACTTCAATATTGGTATTTGGTGATCATGTGACATGTCTATGTAAAGAAGAATGTGTACCAAAGCAGGTTGAAACTGCAGAAACATAGA

Reverse complement sequence

TCTATGTTTCTGCAGTTTCAACCTGCTTTGGTACACATTCTTCTTTACATAGACATGTCACATGATCACCAAATACCAATATTGAAGTCTGAATCATTTT[G/T]
TGTACACAAGAATACAGGATTATAGTTGAAGCATGCGGCTATATAATCATATTATTATTCAGAGCATCAGATGTAACTGAAAAACAATTAATTTGTTCTA

Allele Frequencies:

Populations	Population Size	Frequency of C(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	99.70%	0.20%	0.04%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.60%	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	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
vg0703433196	C -> A	LOC_Os07g06960.1	upstream_gene_variant ; 4729.0bp to feature; MODIFIER	N	Average:53.395; most accessible tissue: Callus, score: 70.013	N	N	N	N
vg0703433196	C -> A	LOC_Os07g06980.1	downstream_gene_variant ; 2737.0bp to feature; MODIFIER	N	Average:53.395; most accessible tissue: Callus, score: 70.013	N	N	N	N
vg0703433196	C -> A	LOC_Os07g06980.2	downstream_gene_variant ; 2737.0bp to feature; MODIFIER	N	Average:53.395; most accessible tissue: Callus, score: 70.013	N	N	N	N
vg0703433196	C -> A	LOC_Os07g06970.1	intron_variant ; MODIFIER	N	Average:53.395; most accessible tissue: Callus, score: 70.013	N	N	N	N