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Detailed information for vg1101692786:

Variant ID: vg1101692786 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 1692786
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: Unkown

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:

CCGAGGCCGACATCTGGAGCATCGGCGTCATGCTCTACATCTTCCTCGCCGGCGTGCCGCCCTTCTGGGCCGAGTCGGAGAACGCCATCTTCACCGCCAT[C/T]
CTTCGCGGACAGATCGACCTCGCCAGTGAGCCATGGCCGAAGATCTCCTCTGGAGCCAAGGACCTCGTCAGGAAGATGCTCAACATCAACCCCAAGGAGA

Reverse complement sequence

TCTCCTTGGGGTTGATGTTGAGCATCTTCCTGACGAGGTCCTTGGCTCCAGAGGAGATCTTCGGCCATGGCTCACTGGCGAGGTCGATCTGTCCGCGAAG[G/A]
ATGGCGGTGAAGATGGCGTTCTCCGACTCGGCCCAGAAGGGCGGCACGCCGGCGAGGAAGATGTAGAGCATGACGCCGATGCTCCAGATGTCGGCCTCGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of Unkown(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.70%	0.00%	0.32%	0.00%	NA
All Indica	2759	99.60%	0.00%	0.36%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	98.10%	0.00%	1.86%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.00%	0.65%	0.00%	NA
Indica III	913	99.60%	0.00%	0.44%	0.00%	NA
Indica Intermediate	786	99.60%	0.00%	0.38%	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
vg1101692786	C -> T	LOC_Os11g04170.1	synonymous_variant ; p.Ile295Ile; LOW	N	Average:69.695; most accessible tissue: Zhenshan97 panicle, score: 87.451	N	N	N	N
vg1101692786	C -> T	LOC_Os11g04150.1	upstream_gene_variant ; 4687.0bp to feature; MODIFIER	N	Average:69.695; most accessible tissue: Zhenshan97 panicle, score: 87.451	N	N	N	N
vg1101692786	C -> T	LOC_Os11g04160.1	downstream_gene_variant ; 1446.0bp to feature; MODIFIER	N	Average:69.695; most accessible tissue: Zhenshan97 panicle, score: 87.451	N	N	N	N
vg1101692786	C -> T	LOC_Os11g04174.1	downstream_gene_variant ; 1686.0bp to feature; MODIFIER	N	Average:69.695; most accessible tissue: Zhenshan97 panicle, score: 87.451	N	N	N	N
vg1101692786	C -> T	LOC_Os11g04180.1	downstream_gene_variant ; 3641.0bp to feature; MODIFIER	N	Average:69.695; most accessible tissue: Zhenshan97 panicle, score: 87.451	N	N	N	N