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Detailed information for vg1100674220:

Variant ID: vg1100674220 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 674220
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

CGTAAGAACTTTGAGTCGTATTAAACTATTAATGTATTGATACGCAGCAGATGGGAGATAATCTTCTTCTTGTTCTGAAATGTGCCTGTTCCACTGAGAG[T/C]
CCTCGTTTTTGAGTATGTCACAATCATTGTGGTTAGGACTTTGGAGAAGTGCATTGTTTCCCAACATGCATCAGACAAAATGAAAATATTGGGTTTCTAT

Reverse complement sequence

ATAGAAACCCAATATTTTCATTTTGTCTGATGCATGTTGGGAAACAATGCACTTCTCCAAAGTCCTAACCACAATGATTGTGACATACTCAAAAACGAGG[A/G]
CTCTCAGTGGAACAGGCACATTTCAGAACAAGAAGAAGATTATCTCCCATCTGCTGCGTATCAATACATTAATAGTTTAATACGACTCAAAGTTCTTACG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.70%	0.20%	0.08%	0.00%	NA
All Indica	2759	99.50%	0.40%	0.14%	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	98.20%	1.20%	0.67%	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%	0.50%	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
vg1100674220	T -> C	LOC_Os11g02310.1	3_prime_UTR_variant ; 1012.0bp to feature; MODIFIER	N	Average:44.604; most accessible tissue: Callus, score: 62.682	N	N	N	N
vg1100674220	T -> C	LOC_Os11g02320.1	upstream_gene_variant ; 2519.0bp to feature; MODIFIER	N	Average:44.604; most accessible tissue: Callus, score: 62.682	N	N	N	N
vg1100674220	T -> C	LOC_Os11g02320.2	upstream_gene_variant ; 2519.0bp to feature; MODIFIER	N	Average:44.604; most accessible tissue: Callus, score: 62.682	N	N	N	N
vg1100674220	T -> C	LOC_Os11g02320.3	upstream_gene_variant ; 2519.0bp to feature; MODIFIER	N	Average:44.604; most accessible tissue: Callus, score: 62.682	N	N	N	N