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Detailed information for vg0626641166:

Variant ID: vg0626641166 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 26641166
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTCATTAGAGTTCACATGAAAAAGTTATGAATTATTTTTAAATATAAAGTCTTTAGACCGTCCTATTTGACCCAGATGATATTAAAATCCAAGTTTAG[G/A]
GACCGGGGTGACACAACTGAACAAGTTGGAGGACCTAAACGAGTGATCTGCAAGTTTAGGGACCGGGATGATACAGTCAAACAAGTTTGAGGACCTGAAC

Reverse complement sequence

GTTCAGGTCCTCAAACTTGTTTGACTGTATCATCCCGGTCCCTAAACTTGCAGATCACTCGTTTAGGTCCTCCAACTTGTTCAGTTGTGTCACCCCGGTC[C/T]
CTAAACTTGGATTTTAATATCATCTGGGTCAAATAGGACGGTCTAAAGACTTTATATTTAAAAATAATTCATAACTTTTTCATGTGAACTCTAATGAAGA

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	88.90%	11.00%	0.08%	0.00%	NA
All Indica	2759	85.40%	14.50%	0.07%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.13%	0.00%	NA
Aus	269	58.40%	41.60%	0.00%	0.00%	NA
Indica I	595	97.10%	2.90%	0.00%	0.00%	NA
Indica II	465	82.80%	17.00%	0.22%	0.00%	NA
Indica III	913	76.90%	23.10%	0.00%	0.00%	NA
Indica Intermediate	786	87.90%	12.00%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.00%	0.40%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0626641166	G -> A	LOC_Os06g44150.1	upstream_gene_variant ; 1409.0bp to feature; MODIFIER	silent_mutation	Average:25.704; most accessible tissue: Zhenshan97 flower, score: 63.813	N	N	N	N
vg0626641166	G -> A	LOC_Os06g44150-LOC_Os06g44160	intergenic_region ; MODIFIER	silent_mutation	Average:25.704; most accessible tissue: Zhenshan97 flower, score: 63.813	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0626641166	5.68E-06	5.68E-06	mr1747	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