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Detailed information for vg0903405239:

Variant ID: vg0903405239 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 3405239
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

GTAGAATGTTAGAAAAGTAGAGAAGTATCTCTTGTTAGGTTATATGAGTCAAATTCTGTACAAAGATGCCCAGCTCAGATGCACTGCACTCTAATGAAAA[A/T]
TAAAACAATCTGAAATCAAGTTCTTATCTTCTATCCATTCTACGTCCCCTCTTCTTTATTACTAGACAGAGATAACATGGAAATAACTTTGGCGATAAGA

Reverse complement sequence

TCTTATCGCCAAAGTTATTTCCATGTTATCTCTGTCTAGTAATAAAGAAGAGGGGACGTAGAATGGATAGAAGATAAGAACTTGATTTCAGATTGTTTTA[T/A]
TTTTCATTAGAGTGCAGTGCATCTGAGCTGGGCATCTTTGTACAGAATTTGACTCATATAACCTAACAAGAGATACTTCTCTACTTTTCTAACATTCTAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.60%	0.40%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	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	100.00%	0.00%	0.00%	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	100.00%	0.00%	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	80.20%	19.80%	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
vg0903405239	A -> T	LOC_Os09g07010.1	upstream_gene_variant ; 2130.0bp to feature; MODIFIER	silent_mutation	Average:55.837; most accessible tissue: Callus, score: 84.863	N	N	N	N
vg0903405239	A -> T	LOC_Os09g07030.1	downstream_gene_variant ; 3641.0bp to feature; MODIFIER	silent_mutation	Average:55.837; most accessible tissue: Callus, score: 84.863	N	N	N	N
vg0903405239	A -> T	LOC_Os09g07020.1	intron_variant ; MODIFIER	silent_mutation	Average:55.837; most accessible tissue: Callus, score: 84.863	N	N	N	N
vg0903405239	A -> T	LOC_Os09g07020.2	intron_variant ; MODIFIER	silent_mutation	Average:55.837; most accessible tissue: Callus, score: 84.863	N	N	N	N