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Detailed information for vg1100782434:

Variant ID: vg1100782434 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 782434
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.01, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:

TTATACACATGCTTCTTAATTTCAGGTTTACTTCTTAGTCATGAGCAAAATGCTATGTATTTTTACCAGGTCACAACTTATCATTACAGCACATCCTGGA[T/A]
GAAACTCCAAGCTAGCTTATAGCTAACATCAAGTCATCATCCCCATATGCATATTGGACTGTGCTCACATCTTATTGAATCATCGAACGTCCAATGCTCA

Reverse complement sequence

TGAGCATTGGACGTTCGATGATTCAATAAGATGTGAGCACAGTCCAATATGCATATGGGGATGATGACTTGATGTTAGCTATAAGCTAGCTTGGAGTTTC[A/T]
TCCAGGATGTGCTGTAATGATAAGTTGTGACCTGGTAAAAATACATAGCATTTTGCTCATGACTAAGAAGTAAACCTGAAATTAAGAAGCATGTGTATAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.70%	0.30%	0.00%	0.00%	NA
All Indica	2759	99.50%	0.50%	0.00%	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	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	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
vg1100782434	T -> A	LOC_Os11g02520.1	3_prime_UTR_variant ; 37.0bp to feature; MODIFIER	N	Average:40.02; most accessible tissue: Minghui63 young leaf, score: 58.21	N	N	N	N
vg1100782434	T -> A	LOC_Os11g02500.1	downstream_gene_variant ; 4865.0bp to feature; MODIFIER	N	Average:40.02; most accessible tissue: Minghui63 young leaf, score: 58.21	N	N	N	N
vg1100782434	T -> A	LOC_Os11g02510.1	downstream_gene_variant ; 3672.0bp to feature; MODIFIER	N	Average:40.02; most accessible tissue: Minghui63 young leaf, score: 58.21	N	N	N	N