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Detailed information for vg0500377108:

Variant ID: vg0500377108 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 377108
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 359. )

Flanking Sequence (100 bp) in Reference Genome:

GCGCAGAGGACACCAATGAAAGTGACTTCGTCTGGTAGCAGCCCATGTTGATCGTCTAGATCATTCCTTGAAAAGGTAGGTGTAAGATCAATAAGGAACT[A/G]
GAAATAACATGGAACAAAATAAGTAGCAGGATATTGCTATCTTGACCAATCTCAGAAATCAGAACCCACCTTGTCCAATCATGTCATGAAACAATCGAAT

Reverse complement sequence

ATTCGATTGTTTCATGACATGATTGGACAAGGTGGGTTCTGATTTCTGAGATTGGTCAAGATAGCAATATCCTGCTACTTATTTTGTTCCATGTTATTTC[T/C]
AGTTCCTTATTGATCTTACACCTACCTTTTCAAGGAATGATCTAGACGATCAACATGGGCTGCTACCAGACGAAGTCACTTTCATTGGTGTCCTCTGCGC

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	99.00%	1.00%	0.00%	0.00%	NA
All Indica	2759	98.40%	1.60%	0.00%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	98.90%	1.10%	0.00%	0.00%	NA
Indica Intermediate	786	96.30%	3.70%	0.00%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	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
vg0500377108	A -> G	LOC_Os05g01630.1	upstream_gene_variant ; 1425.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500377108	A -> G	LOC_Os05g01640.1	upstream_gene_variant ; 4066.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500377108	A -> G	LOC_Os05g01630.2	upstream_gene_variant ; 1425.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500377108	A -> G	LOC_Os05g01630.3	upstream_gene_variant ; 1425.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500377108	A -> G	LOC_Os05g01635.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N