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Detailed information for vg0500376139:

Variant ID: vg0500376139 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 376139
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

TTAATATAACATATATCCCTTTCTTCTATGCCACAAAAGACAAAGCCCAAACCAGATGAACGCAGGCGCTAGTTATCGAGAGCATTTATAAAGTGAATGA[G/A]
AATTCTCTCTATTCATATAATTGTCTTCCACTGGCACTAAGCAAGTGTATATTCAGAGACTTGCTGTTTGGTGCATATGTATGTATGTGATGTGCACATA

Reverse complement sequence

TATGTGCACATCACATACATACATATGCACCAAACAGCAAGTCTCTGAATATACACTTGCTTAGTGCCAGTGGAAGACAATTATATGAATAGAGAGAATT[C/T]
TCATTCACTTTATAAATGCTCTCGATAACTAGCGCCTGCGTTCATCTGGTTTGGGCTTTGTCTTTTGTGGCATAGAAGAAAGGGATATATGTTATATTAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.50%	0.50%	0.00%	0.00%	NA
All Indica	2759	99.60%	0.40%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	94.80%	5.20%	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	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	98.90%	1.10%	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
vg0500376139	G -> A	LOC_Os05g01635.1	3_prime_UTR_variant ; 331.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500376139	G -> A	LOC_Os05g01630.1	upstream_gene_variant ; 456.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500376139	G -> A	LOC_Os05g01630.2	upstream_gene_variant ; 456.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500376139	G -> A	LOC_Os05g01630.3	upstream_gene_variant ; 456.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N