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Detailed information for vg0418997871:

Variant ID: vg0418997871 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 18997871
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

ATTGATATTTGCTAGTATATATTTCCTAATTTTATATTTGTAAAGCATTAAGCATATTCCAAAATTCACAATGAATGCAACCGAGGGTCAGGGGTGCCAA[A/T]
TTTGTCTTAGTTATTTCTGAATTCATCCTGGAATCAAATTGTTTCCACAGCTGCATTACCTGAAACTGAAACCTCCCAAATTTCAGTTCAAAACGAGCTG

Reverse complement sequence

CAGCTCGTTTTGAACTGAAATTTGGGAGGTTTCAGTTTCAGGTAATGCAGCTGTGGAAACAATTTGATTCCAGGATGAATTCAGAAATAACTAAGACAAA[T/A]
TTGGCACCCCTGACCCTCGGTTGCATTCATTGTGAATTTTGGAATATGCTTAATGCTTTACAAATATAAAATTAGGAAATATATACTAGCAAATATCAAT

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	97.40%	2.60%	0.00%	0.00%	NA
All Indica	2759	95.60%	4.40%	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	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	95.90%	4.10%	0.00%	0.00%	NA
Indica III	913	92.30%	7.70%	0.00%	0.00%	NA
Indica Intermediate	786	96.40%	3.60%	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
vg0418997871	A -> T	LOC_Os04g31730.1	3_prime_UTR_variant ; 155.0bp to feature; MODIFIER	silent_mutation	Average:61.903; most accessible tissue: Callus, score: 74.819	N	N	N	N
vg0418997871	A -> T	LOC_Os04g31700.1	upstream_gene_variant ; 4940.0bp to feature; MODIFIER	silent_mutation	Average:61.903; most accessible tissue: Callus, score: 74.819	N	N	N	N
vg0418997871	A -> T	LOC_Os04g31740.1	upstream_gene_variant ; 3480.0bp to feature; MODIFIER	silent_mutation	Average:61.903; most accessible tissue: Callus, score: 74.819	N	N	N	N
vg0418997871	A -> T	LOC_Os04g31710.1	downstream_gene_variant ; 2180.0bp to feature; MODIFIER	silent_mutation	Average:61.903; most accessible tissue: Callus, score: 74.819	N	N	N	N
vg0418997871	A -> T	LOC_Os04g31720.1	downstream_gene_variant ; 1295.0bp to feature; MODIFIER	silent_mutation	Average:61.903; most accessible tissue: Callus, score: 74.819	N	N	N	N