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Detailed information for vg0726455116:

Variant ID: vg0726455116 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 26455116
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:

CGCCCATTTATGAAGGGATGACAGGGTGATCTCCGAGGTTAGACGAGCGAGGACGCCTGGCCACACTCAAGAACAAGCTGTGTTTTAGCTTCCAAGAGAA[G/A]
GCGAGCCAAGTTTTGGTGAAGATAGGATGGGTCCCCACCCAAAAGAAAAGTAGGTAGAAGTGGAGCATGTGGGATCCCCTTGAGTTATAAAAGGAGGACC

Reverse complement sequence

GGTCCTCCTTTTATAACTCAAGGGGATCCCACATGCTCCACTTCTACCTACTTTTCTTTTGGGTGGGGACCCATCCTATCTTCACCAAAACTTGGCTCGC[C/T]
TTCTCTTGGAAGCTAAAACACAGCTTGTTCTTGAGTGTGGCCAGGCGTCCTCGCTCGTCTAACCTCGGAGATCACCCTGTCATCCCTTCATAAATGGGCG

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	58.90%	1.00%	10.47%	29.62%	NA
All Indica	2759	52.20%	1.60%	16.42%	29.83%	NA
All Japonica	1512	71.10%	0.10%	1.06%	27.71%	NA
Aus	269	47.60%	0.70%	6.69%	44.98%	NA
Indica I	595	71.40%	0.20%	2.86%	25.55%	NA
Indica II	465	25.40%	2.80%	34.41%	37.42%	NA
Indica III	913	54.40%	1.60%	14.79%	29.13%	NA
Indica Intermediate	786	50.90%	1.80%	17.94%	29.39%	NA
Temperate Japonica	767	93.70%	0.00%	0.39%	5.87%	NA
Tropical Japonica	504	36.90%	0.20%	1.59%	61.31%	NA
Japonica Intermediate	241	70.50%	0.40%	2.07%	26.97%	NA
VI/Aromatic	96	80.20%	0.00%	3.12%	16.67%	NA
Intermediate	90	70.00%	1.10%	5.56%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0726455116	G -> DEL	N	N	silent_mutation	Average:35.746; most accessible tissue: Zhenshan97 root, score: 68.908	N	N	N	N
vg0726455116	G -> A	LOC_Os07g44260.1	upstream_gene_variant ; 4646.0bp to feature; MODIFIER	silent_mutation	Average:35.746; most accessible tissue: Zhenshan97 root, score: 68.908	N	N	N	N
vg0726455116	G -> A	LOC_Os07g44280.1	downstream_gene_variant ; 1605.0bp to feature; MODIFIER	silent_mutation	Average:35.746; most accessible tissue: Zhenshan97 root, score: 68.908	N	N	N	N
vg0726455116	G -> A	LOC_Os07g44260-LOC_Os07g44280	intergenic_region ; MODIFIER	silent_mutation	Average:35.746; most accessible tissue: Zhenshan97 root, score: 68.908	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0726455116	NA	3.11E-11	mr1746	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
vg0726455116	NA	9.81E-08	mr1928	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
vg0726455116	1.70E-06	NA	mr1746_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