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Detailed information for vg0334134799:

Variant ID: vg0334134799 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34134799
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 363. )

Flanking Sequence (100 bp) in Reference Genome:

ACACAACATGTTTCCTTTCGAGAGGTACATGGGCGTTCTGAAGAAGTATGTTCGTAACCGTGCTCGTCCAGAGGCAAGCATCGCCAAGGGTTATGGAACA[G/T]
AGGAGGTCATCGAATTTTGCGTAGAATTTATCGAAGACCTTCGCCCAATCGGGGTACCTGAATCACGCCATGAAGGGAGACTACGGGGAAAGGGAACTCT

Reverse complement sequence

AGAGTTCCCTTTCCCCGTAGTCTCCCTTCATGGCGTGATTCAGGTACCCCGATTGGGCGAAGGTCTTCGATAAATTCTACGCAAAATTCGATGACCTCCT[C/A]
TGTTCCATAACCCTTGGCGATGCTTGCCTCTGGACGAGCACGGTTACGAACATACTTCTTCAGAACGCCCATGTACCTCTCGAAAGGAAACATGTTGTGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	1.00%	0.40%	5.50%	93.06%	NA
All Indica	2759	1.10%	0.70%	7.43%	90.79%	NA
All Japonica	1512	0.30%	0.10%	0.60%	99.07%	NA
Aus	269	4.80%	0.00%	16.36%	78.81%	NA
Indica I	595	0.80%	0.00%	4.03%	95.13%	NA
Indica II	465	0.60%	0.20%	2.58%	96.56%	NA
Indica III	913	0.80%	1.50%	15.22%	82.48%	NA
Indica Intermediate	786	2.00%	0.40%	3.82%	93.77%	NA
Temperate Japonica	767	0.10%	0.00%	0.26%	99.61%	NA
Tropical Japonica	504	0.40%	0.00%	1.19%	98.41%	NA
Japonica Intermediate	241	0.40%	0.40%	0.41%	98.76%	NA
VI/Aromatic	96	0.00%	0.00%	0.00%	100.00%	NA
Intermediate	90	1.10%	0.00%	2.22%	96.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0334134799	G -> T	LOC_Os03g60010.1	stop_gained ; p.Glu790*; HIGH	stop_gained	Average:5.718; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N
vg0334134799	G -> DEL	LOC_Os03g60010.1	N	frameshift_variant	Average:5.718; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N