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Detailed information for vg1100673679:

Variant ID: vg1100673679 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 673679
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCAGATGGACATATGTGTGATGGCACTGGAAAATTAACCGATACCGAATGGTTTTGTTGGTCAACAACAAATGTTTCTGAAACTGAATCATGAATCCG[G/T]
GCTAATTGAATGTTTTAGACATGAATAACTGGCAGCAAAATAATTACTCACATCATTGCCCCTTCACTCATATCACTCAGTACCAAAGGTTCGGACAGAA

Reverse complement sequence

TTCTGTCCGAACCTTTGGTACTGAGTGATATGAGTGAAGGGGCAATGATGTGAGTAATTATTTTGCTGCCAGTTATTCATGTCTAAAACATTCAATTAGC[C/A]
CGGATTCATGATTCAGTTTCAGAAACATTTGTTGTTGACCAACAAAACCATTCGGTATCGGTTAATTTTCCAGTGCCATCACACATATGTCCATCTGGAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.80%	0.10%	0.06%	0.00%	NA
All Indica	2759	99.60%	0.30%	0.11%	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	99.00%	0.70%	0.34%	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	99.50%	0.40%	0.13%	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
vg1100673679	G -> T	LOC_Os11g02310.1	3_prime_UTR_variant ; 471.0bp to feature; MODIFIER	N	Average:37.945; most accessible tissue: Callus, score: 66.487	N	N	N	N
vg1100673679	G -> T	LOC_Os11g02320.1	upstream_gene_variant ; 1978.0bp to feature; MODIFIER	N	Average:37.945; most accessible tissue: Callus, score: 66.487	N	N	N	N
vg1100673679	G -> T	LOC_Os11g02320.2	upstream_gene_variant ; 1978.0bp to feature; MODIFIER	N	Average:37.945; most accessible tissue: Callus, score: 66.487	N	N	N	N
vg1100673679	G -> T	LOC_Os11g02320.3	upstream_gene_variant ; 1978.0bp to feature; MODIFIER	N	Average:37.945; most accessible tissue: Callus, score: 66.487	N	N	N	N