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Detailed information for vg0629288529:

Variant ID: vg0629288529 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 29288529
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

TTATGCTCACTTTCGAGTTGCATGGCTTTGTCCACAAGTTTCTCAAAATCTTCATAATCCTCTAGGAGTAGTTGCACTGCGAGCTCATCTTTTAACCCCT[G/A]
GAGAAACTTCTCTTGTTTGTCTTCATCCGTTTCCACGTCTTCTGGTGCATAGTGAGCCAAACGATAGAACTCGTGCAGGTACTCTGTGACGGTCAAATCT

Reverse complement sequence

AGATTTGACCGTCACAGAGTACCTGCACGAGTTCTATCGTTTGGCTCACTATGCACCAGAAGACGTGGAAACGGATGAAGACAAACAAGAGAAGTTTCTC[C/T]
AGGGGTTAAAAGATGAGCTCGCAGTGCAACTACTCCTAGAGGATTATGAAGATTTTGAGAAACTTGTGGACAAAGCCATGCAACTCGAAAGTGAGCATAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	26.10%	0.10%	9.86%	63.88%	NA
All Indica	2759	2.80%	0.10%	10.15%	86.95%	NA
All Japonica	1512	66.60%	0.10%	5.56%	27.78%	NA
Aus	269	42.00%	0.70%	23.05%	34.20%	NA
Indica I	595	1.70%	0.00%	3.03%	95.29%	NA
Indica II	465	3.00%	0.00%	11.83%	85.16%	NA
Indica III	913	2.00%	0.00%	12.60%	85.43%	NA
Indica Intermediate	786	4.50%	0.40%	11.70%	83.46%	NA
Temperate Japonica	767	67.30%	0.00%	4.82%	27.90%	NA
Tropical Japonica	504	68.80%	0.00%	4.96%	26.19%	NA
Japonica Intermediate	241	59.80%	0.40%	9.13%	30.71%	NA
VI/Aromatic	96	8.30%	0.00%	35.42%	56.25%	NA
Intermediate	90	33.30%	0.00%	6.67%	60.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0629288529	G -> A	LOC_Os06g48420.1	stop_gained ; p.Gln212*; HIGH	stop_gained	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0629288529	G -> DEL	LOC_Os06g48420.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N