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Detailed information for vg0420225156:

Variant ID: vg0420225156 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 20225156
Reference Allele: TG	Alternative Allele: T
Primary Allele: TG	Secondary Allele: T

Inferred Ancestral Allele : TG (evidence from allele frequency in Oryza rufipogon: TG: 0.99, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

TTCAGTCCCTTGTTGACCTCCTCAATGACTACATTGTTCTGAAGACCAGAAAACAAATCTATCAAGCACTATGCATGACAAAAGGGCACTGCAATTTAAA[TG/T]
TATGTGACTTCTTTATCGAAAAAATACTATGAGGCTTGCAGGGTTAGAAGAAGTTAACCCTTCCATAGGAGTATATGTTACAAGTTACTAGACACATAGA

Reverse complement sequence

TCTATGTGTCTAGTAACTTGTAACATATACTCCTATGGAAGGGTTAACTTCTTCTAACCCTGCAAGCCTCATAGTATTTTTTCGATAAAGAAGTCACATA[CA/A]
TTTAAATTGCAGTGCCCTTTTGTCATGCATAGTGCTTGATAGATTTGTTTTCTGGTCTTCAGAACAATGTAGTCATTGAGGAGGTCAACAAGGGACTGAA

Allele Frequencies:

Populations	Population Size	Frequency of TG(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.50%	0.50%	0.00%	0.00%	NA
All Indica	2759	99.20%	0.80%	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	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	98.60%	1.40%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.60%	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
vg0420225156	TG -> T	LOC_Os04g33450.1	upstream_gene_variant ; 2083.0bp to feature; MODIFIER	N	Average:67.593; most accessible tissue: Zhenshan97 flower, score: 85.141	N	N	N	N
vg0420225156	TG -> T	LOC_Os04g33450.3	upstream_gene_variant ; 2083.0bp to feature; MODIFIER	N	Average:67.593; most accessible tissue: Zhenshan97 flower, score: 85.141	N	N	N	N
vg0420225156	TG -> T	LOC_Os04g33450.2	upstream_gene_variant ; 2075.0bp to feature; MODIFIER	N	Average:67.593; most accessible tissue: Zhenshan97 flower, score: 85.141	N	N	N	N
vg0420225156	TG -> T	LOC_Os04g33430.1	downstream_gene_variant ; 1727.0bp to feature; MODIFIER	N	Average:67.593; most accessible tissue: Zhenshan97 flower, score: 85.141	N	N	N	N
vg0420225156	TG -> T	LOC_Os04g33420.1	downstream_gene_variant ; 4065.0bp to feature; MODIFIER	N	Average:67.593; most accessible tissue: Zhenshan97 flower, score: 85.141	N	N	N	N
vg0420225156	TG -> T	LOC_Os04g33440.2	intron_variant ; MODIFIER	N	Average:67.593; most accessible tissue: Zhenshan97 flower, score: 85.141	N	N	N	N