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Detailed information for vg0614537609:

Variant ID: vg0614537609 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14537609
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: 295. )

Flanking Sequence (100 bp) in Reference Genome:

AATGAGAAGAGGTCGGGGGAAAGACTCCGTTTAAATAGAATGGTGGAACTCAAAAGTCGGAGGTAAACGAGCGCTAAAAATAGAATGCCGTGGCGCCATC[G/A]
CGAAAATTGTTTACTCATGTGAAAACGGCGCAAAAATGGCGCCATGCCCAGCTGAAACATGCATGCAAAATCCGAGTGGTTTCGAACCTGCGACCTTGGG

Reverse complement sequence

CCCAAGGTCGCAGGTTCGAAACCACTCGGATTTTGCATGCATGTTTCAGCTGGGCATGGCGCCATTTTTGCGCCGTTTTCACATGAGTAAACAATTTTCG[C/T]
GATGGCGCCACGGCATTCTATTTTTAGCGCTCGTTTACCTCCGACTTTTGAGTTCCACCATTCTATTTAAACGGAGTCTTTCCCCCGACCTCTTCTCATT

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	96.60%	2.80%	0.59%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.07%	0.00%	NA
All Japonica	1512	90.50%	7.90%	1.59%	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	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.50%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.30%	0.13%	0.00%	NA
Tropical Japonica	504	77.00%	20.40%	2.58%	0.00%	NA
Japonica Intermediate	241	89.60%	6.20%	4.15%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	6.70%	2.22%	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
vg0614537609	G -> A	LOC_Os06g24750.1	upstream_gene_variant ; 159.0bp to feature; MODIFIER	silent_mutation	Average:42.615; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N
vg0614537609	G -> A	LOC_Os06g24760.1	upstream_gene_variant ; 640.0bp to feature; MODIFIER	silent_mutation	Average:42.615; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N
vg0614537609	G -> A	LOC_Os06g24750-LOC_Os06g24760	intergenic_region ; MODIFIER	silent_mutation	Average:42.615; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614537609	NA	9.64E-06	mr1159	Jap_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
vg0614537609	NA	6.72E-06	mr1217_2	Jap_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
vg0614537609	NA	6.40E-06	mr1228_2	Jap_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
vg0614537609	4.29E-06	1.17E-07	mr1606_2	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
vg0614537609	NA	9.38E-06	mr1707_2	Jap_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
vg0614537609	NA	8.93E-06	mr1818_2	Jap_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