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Detailed information for vg0626806805:

Variant ID: vg0626806805 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 26806805
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, T: 0.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CTGTTCAGTTATTTCTTCCAGGTGGGTTTCCTCCTTGATTCTTGCGCTCCCTCGATCGGAATCGCCGGTCAGGTGTTTCGTCGAACGGGTGGTGGGCGTC[G/T]
AGCTGGTGGGGGTTTTGCGTTGTTCCCGGCGTGTTTCTTGTTTGATCGGGGGTGGTTCGTGATTCTTGAAGCGGAAGGGTTGATCTTGGCTTACTCCGGG

Reverse complement sequence

CCCGGAGTAAGCCAAGATCAACCCTTCCGCTTCAAGAATCACGAACCACCCCCGATCAAACAAGAAACACGCCGGGAACAACGCAAAACCCCCACCAGCT[C/A]
GACGCCCACCACCCGTTCGACGAAACACCTGACCGGCGATTCCGATCGAGGGAGCGCAAGAATCAAGGAGGAAACCCACCTGGAAGAAATAACTGAACAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.50%	27.40%	0.13%	0.00%	NA
All Indica	2759	55.70%	44.10%	0.18%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	79.20%	20.80%	0.00%	0.00%	NA
Indica I	595	42.90%	57.10%	0.00%	0.00%	NA
Indica II	465	29.00%	70.80%	0.22%	0.00%	NA
Indica III	913	72.90%	26.70%	0.33%	0.00%	NA
Indica Intermediate	786	61.30%	38.50%	0.13%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	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	84.40%	14.40%	1.11%	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
vg0626806805	G -> T	LOC_Os06g44400.1	upstream_gene_variant ; 3439.0bp to feature; MODIFIER	silent_mutation	Average:63.956; most accessible tissue: Zhenshan97 root, score: 83.426	N	N	N	N
vg0626806805	G -> T	LOC_Os06g44410.1	upstream_gene_variant ; 1056.0bp to feature; MODIFIER	silent_mutation	Average:63.956; most accessible tissue: Zhenshan97 root, score: 83.426	N	N	N	N
vg0626806805	G -> T	LOC_Os06g44400-LOC_Os06g44410	intergenic_region ; MODIFIER	silent_mutation	Average:63.956; most accessible tissue: Zhenshan97 root, score: 83.426	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0626806805	2.62E-06	NA	mr1743	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
vg0626806805	7.06E-06	8.16E-07	mr1743	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251