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Detailed information for vg0906481589:

Variant ID: vg0906481589 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6481589
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

TCACAACCTGAGAGGTGGCTGATACGTATAGTAATAGCGGTTCTTGTGGGTGTGGTGAGGCCAAAACTAGTGGAGTAGTAAGAAGTTTCTTGAAATCTTC[A/G]
AAGGCTTTCTGTGCTTCAGGTCCCCACTGGAAATTGTCTGTTTTCTTTAACAGTTTGAAGAAGGGCATCCCCCGCTCGCCGAGTCGTGAGACAAACCGGC

Reverse complement sequence

GCCGGTTTGTCTCACGACTCGGCGAGCGGGGGATGCCCTTCTTCAAACTGTTAAAGAAAACAGACAATTTCCAGTGGGGACCTGAAGCACAGAAAGCCTT[T/C]
GAAGATTTCAAGAAACTTCTTACTACTCCACTAGTTTTGGCCTCACCACACCCACAAGAACCGCTATTACTATACGTATCAGCCACCTCTCAGGTTGTGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.40%	0.10%	46.15%	5.33%	NA
All Indica	2759	24.10%	0.20%	67.23%	8.45%	NA
All Japonica	1512	98.40%	0.00%	1.52%	0.07%	NA
Aus	269	18.20%	0.00%	76.58%	5.20%	NA
Indica I	595	33.30%	0.00%	44.37%	22.35%	NA
Indica II	465	23.20%	0.00%	70.97%	5.81%	NA
Indica III	913	14.30%	0.20%	84.12%	1.31%	NA
Indica Intermediate	786	29.00%	0.50%	62.72%	7.76%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	99.20%	0.00%	0.79%	0.00%	NA
Japonica Intermediate	241	92.50%	0.00%	7.47%	0.00%	NA
VI/Aromatic	96	28.10%	0.00%	71.88%	0.00%	NA
Intermediate	90	64.40%	0.00%	31.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906481589	A -> G	LOC_Os09g11610.1	synonymous_variant ; p.Phe706Phe; LOW	synonymous_codon	Average:34.94; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg0906481589	A -> DEL	LOC_Os09g11610.1	N	frameshift_variant	Average:34.94; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906481589	3.97E-06	8.42E-07	mr1168	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251