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Detailed information for vg0915839206:

Variant ID: vg0915839206 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 15839206
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

CAACCAAACTTCCAATTTTTATGTGAACTAAACACAGCCCCTATATGTTCCCTTGCTCTCTTTTACTACTCCCTCCGTCCCATAATATAAGGGATTTTGA[G/A]
TTTTTGCTTGCAACTTTTGATCACTCGTTTTATTAAAAAAAATTATAATTATTATTTATTTTATTTGTGATTTACTTTATTATCTACAGTACTTTAAGCA

Reverse complement sequence

TGCTTAAAGTACTGTAGATAATAAAGTAAATCACAAATAAAATAAATAATAATTATAATTTTTTTTAATAAAACGAGTGATCAAAAGTTGCAAGCAAAAA[C/T]
TCAAAATCCCTTATATTATGGGACGGAGGGAGTAGTAAAAGAGAGCAAGGGAACATATAGGGGCTGTGTTTAGTTCACATAAAAATTGGAAGTTTGGTTG

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	85.30%	9.20%	0.21%	5.35%	NA
All Indica	2759	81.80%	15.40%	0.36%	2.46%	NA
All Japonica	1512	99.90%	0.00%	0.00%	0.13%	NA
Aus	269	32.00%	0.40%	0.00%	67.66%	NA
Indica I	595	97.10%	0.70%	0.17%	2.02%	NA
Indica II	465	51.20%	46.00%	0.43%	2.37%	NA
Indica III	913	88.10%	10.20%	0.55%	1.20%	NA
Indica Intermediate	786	81.00%	14.40%	0.25%	4.33%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	7.80%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0915839206	G -> DEL	N	N	silent_mutation	Average:40.444; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0915839206	G -> A	LOC_Os09g26220.1	downstream_gene_variant ; 4186.0bp to feature; MODIFIER	silent_mutation	Average:40.444; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0915839206	G -> A	LOC_Os09g26210-LOC_Os09g26220	intergenic_region ; MODIFIER	silent_mutation	Average:40.444; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0915839206	9.77E-08	9.76E-08	mr1848_2	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
vg0915839206	1.02E-06	1.02E-06	mr1848_2	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