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Detailed information for vg0617635655:

Variant ID: vg0617635655 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 17635655
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.01, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

GGATGTAGGGTTATTACCTGACAATTCAGGGCCCGAACCTGTATAAAAATCCCTGTCTCTGTCTCTTTTACCTTAGTCTCGCGTATACTCTAGTACCAAC[G/A]
ATCCCCATACTATGCAAATACCAGAATTGCGACATCAAATGTTGACAGAGATGTGTTCCATATCAAAGTTGTAGAGCTCAACGGGATCTACCACTTTGTA

Reverse complement sequence

TACAAAGTGGTAGATCCCGTTGAGCTCTACAACTTTGATATGGAACACATCTCTGTCAACATTTGATGTCGCAATTCTGGTATTTGCATAGTATGGGGAT[C/T]
GTTGGTACTAGAGTATACGCGAGACTAAGGTAAAAGAGACAGAGACAGGGATTTTTATACAGGTTCGGGCCCTGAATTGTCAGGTAATAACCCTACATCC

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	34.00%	6.90%	0.72%	58.36%	NA
All Indica	2759	5.50%	6.90%	0.94%	86.63%	NA
All Japonica	1512	86.90%	8.60%	0.07%	4.43%	NA
Aus	269	15.60%	0.00%	2.23%	82.16%	NA
Indica I	595	6.60%	3.20%	1.34%	88.91%	NA
Indica II	465	5.60%	2.20%	1.29%	90.97%	NA
Indica III	913	1.60%	13.30%	0.44%	84.67%	NA
Indica Intermediate	786	9.20%	5.20%	1.02%	84.61%	NA
Temperate Japonica	767	93.00%	0.30%	0.13%	6.65%	NA
Tropical Japonica	504	76.20%	22.40%	0.00%	1.39%	NA
Japonica Intermediate	241	90.00%	6.20%	0.00%	3.73%	NA
VI/Aromatic	96	61.50%	0.00%	0.00%	38.54%	NA
Intermediate	90	46.70%	4.40%	1.11%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0617635655	G -> A	LOC_Os06g30500.1	upstream_gene_variant ; 3309.0bp to feature; MODIFIER	silent_mutation	Average:6.13; most accessible tissue: Zhenshan97 flag leaf, score: 9.474	N	N	N	N
vg0617635655	G -> A	LOC_Os06g30510.1	upstream_gene_variant ; 3736.0bp to feature; MODIFIER	silent_mutation	Average:6.13; most accessible tissue: Zhenshan97 flag leaf, score: 9.474	N	N	N	N
vg0617635655	G -> A	LOC_Os06g30500-LOC_Os06g30510	intergenic_region ; MODIFIER	silent_mutation	Average:6.13; most accessible tissue: Zhenshan97 flag leaf, score: 9.474	N	N	N	N
vg0617635655	G -> DEL	N	N	silent_mutation	Average:6.13; most accessible tissue: Zhenshan97 flag leaf, score: 9.474	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0617635655	1.69E-06	NA	mr1798_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