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Detailed information for vg0200790342:

Variant ID: vg0200790342 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 790342
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

AAAACAATCAGCATCATGTAGATGAAATGGAACAATTGAAAATGCTCAATTTTGTTATTCTGTGACAGCTTGAGCTTTGTTTTTTTTAACTTAAAAGACG[T/A]
TGTTTTGTCTGAATTTCAAGGTAAAGTTCAGCTACAAGTTAGAACTAGCTTGGTTTTGTATCATCCTGTTCATAGAGATTGTCAGGTGTGAGGATTACTT

Reverse complement sequence

AAGTAATCCTCACACCTGACAATCTCTATGAACAGGATGATACAAAACCAAGCTAGTTCTAACTTGTAGCTGAACTTTACCTTGAAATTCAGACAAAACA[A/T]
CGTCTTTTAAGTTAAAAAAAACAAAGCTCAAGCTGTCACAGAATAACAAAATTGAGCATTTTCAATTGTTCCATTTCATCTACATGATGCTGATTGTTTT

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	74.10%	25.60%	0.28%	0.04%	NA
All Indica	2759	58.40%	41.10%	0.43%	0.07%	NA
All Japonica	1512	95.80%	4.10%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	66.70%	32.60%	0.50%	0.17%	NA
Indica II	465	64.70%	34.80%	0.43%	0.00%	NA
Indica III	913	41.10%	58.60%	0.33%	0.00%	NA
Indica Intermediate	786	68.60%	30.80%	0.51%	0.13%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	92.70%	7.10%	0.20%	0.00%	NA
Japonica Intermediate	241	90.00%	10.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	15.60%	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
vg0200790342	T -> A	LOC_Os02g02350.2	upstream_gene_variant ; 4666.0bp to feature; MODIFIER	silent_mutation	Average:60.271; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0200790342	T -> A	LOC_Os02g02360.1	downstream_gene_variant ; 1107.0bp to feature; MODIFIER	silent_mutation	Average:60.271; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0200790342	T -> A	LOC_Os02g02380.1	downstream_gene_variant ; 4724.0bp to feature; MODIFIER	silent_mutation	Average:60.271; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0200790342	T -> A	LOC_Os02g02370.1	intron_variant ; MODIFIER	silent_mutation	Average:60.271; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0200790342	T -> DEL	N	N	silent_mutation	Average:60.271; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N