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Detailed information for vg0500377022:

Variant ID: vg0500377022 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 377022
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 368. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCAAATGTTGGCTTGATGTTGTACATGGTGCTCATCTGCTCAAAATATGCCTTCCCGTCATCCAAGAGAGCTAGACGGGTACACGCGCAGAGGACACC[A/T]
ATGAAAGTGACTTCGTCTGGTAGCAGCCCATGTTGATCGTCTAGATCATTCCTTGAAAAGGTAGGTGTAAGATCAATAAGGAACTAGAAATAACATGGAA

Reverse complement sequence

TTCCATGTTATTTCTAGTTCCTTATTGATCTTACACCTACCTTTTCAAGGAATGATCTAGACGATCAACATGGGCTGCTACCAGACGAAGTCACTTTCAT[T/A]
GGTGTCCTCTGCGCGTGTACCCGTCTAGCTCTCTTGGATGACGGGAAGGCATATTTTGAGCAGATGAGCACCATGTACAACATCAAGCCAACATTTGCAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(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	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	99.60%	0.30%	0.07%	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	98.80%	1.00%	0.20%	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
vg0500377022	A -> T	LOC_Os05g01635.1	synonymous_variant ; p.Ile370Ile; LOW	N	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500377022	A -> T	LOC_Os05g01630.1	upstream_gene_variant ; 1339.0bp to feature; MODIFIER	N	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500377022	A -> T	LOC_Os05g01640.1	upstream_gene_variant ; 4152.0bp to feature; MODIFIER	N	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500377022	A -> T	LOC_Os05g01630.2	upstream_gene_variant ; 1339.0bp to feature; MODIFIER	N	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500377022	A -> T	LOC_Os05g01630.3	upstream_gene_variant ; 1339.0bp to feature; MODIFIER	N	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N