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Detailed information for vg0905621216:

Variant ID: vg0905621216 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5621216
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CGCTCCACGCCAACTGCATCCATGGCGCAAAGCATATACACGCCATGCTTCAGAGTGGTGCTATCTTCATCTTCCGGGCAATTGTAAACTCCATACTCCT[G/A]
ATCATGAAGCTTGTGTGGATGATACTGGAAATCTGATGACTCTAACTCCTCATCAAAGCGATGACGAAGCTCTCCAATGGCCACCAAAGCTGCCTCCTGA

Reverse complement sequence

TCAGGAGGCAGCTTTGGTGGCCATTGGAGAGCTTCGTCATCGCTTTGATGAGGAGTTAGAGTCATCAGATTTCCAGTATCATCCACACAAGCTTCATGAT[C/T]
AGGAGTATGGAGTTTACAATTGCCCGGAAGATGAAGATAGCACCACTCTGAAGCATGGCGTGTATATGCTTTGCGCCATGGATGCAGTTGGCGTGGAGCG

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	94.20%	5.80%	0.02%	0.00%	NA
All Indica	2759	94.50%	5.50%	0.04%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	56.90%	43.10%	0.00%	0.00%	NA
Indica I	595	93.30%	6.60%	0.17%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	94.90%	5.10%	0.00%	0.00%	NA
Indica Intermediate	786	91.90%	8.10%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0905621216	G -> A	LOC_Os09g10310.1	stop_gained ; p.Gln105*; HIGH	stop_gained	Average:54.139; most accessible tissue: Zhenshan97 flag leaf, score: 70.425	N	N	N	N