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Detailed information for vg0216167479:

Variant ID: vg0216167479 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 16167479
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: 345. )

Flanking Sequence (100 bp) in Reference Genome:

GTCTGATCCTGACCGTGAAGGGGAAACAATTGCTTGGCATATCAAAGAAATGCTTGAACGACAAGACGCTTTGGGTTGTAATGTTACTGTTGCCAGAGTT[G/A]
TCTTTCATGAAATAACAGAGGATGCTGTTAAAAATGCTTTAATGTCTCCAAGATATATTGATATGAACCTAATTAATGCCTATCTAGCACGACGTTCCCT

Reverse complement sequence

AGGGAACGTCGTGCTAGATAGGCATTAATTAGGTTCATATCAATATATCTTGGAGACATTAAAGCATTTTTAACAGCATCCTCTGTTATTTCATGAAAGA[C/T]
AACTCTGGCAACAGTAACATTACAACCCAAAGCGTCTTGTCGTTCAAGCATTTCTTTGATATGCCAAGCAATTGTTTCCCCTTCACGGTCAGGATCAGAC

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	96.40%	3.20%	0.47%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.04%	0.00%	NA
All Japonica	1512	89.60%	9.20%	1.19%	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	99.80%	0.10%	0.11%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	98.20%	1.30%	0.52%	0.00%	NA
Tropical Japonica	504	74.80%	23.40%	1.79%	0.00%	NA
Japonica Intermediate	241	93.40%	4.60%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	3.30%	3.33%	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
vg0216167479	G -> A	LOC_Os02g27430-LOC_Os02g27440	intergenic_region ; MODIFIER	silent_mutation	Average:45.512; most accessible tissue: Callus, score: 70.905	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0216167479	2.66E-06	NA	mr1550	Jap_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