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Detailed information for vg0114587216:

Variant ID: vg0114587216 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14587216
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: 0.02, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

ACAAGACTTTAGTAAGCTTTAAGAATGGGACACTCCCATTAAGCAAAACTGTGCAAAATTCATACAGCACGAGTGCAATTATCAATCGTACCATTATTGC[G/A]
CTGCTGTCCTGTGAACTTCTCTTATGGGCAGCAATTCCATAGCCACATGCTTATCTTGCACAAACAAATTTTCAAAAATTCATTAATCAATTCTACTGCT

Reverse complement sequence

AGCAGTAGAATTGATTAATGAATTTTTGAAAATTTGTTTGTGCAAGATAAGCATGTGGCTATGGAATTGCTGCCCATAAGAGAAGTTCACAGGACAGCAG[C/T]
GCAATAATGGTACGATTGATAATTGCACTCGTGCTGTATGAATTTTGCACAGTTTTGCTTAATGGGAGTGTCCCATTCTTAAAGCTTACTAAAGTCTTGT

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	60.70%	18.00%	0.68%	20.69%	NA
All Indica	2759	34.00%	30.00%	1.16%	34.83%	NA
All Japonica	1512	99.80%	0.00%	0.00%	0.20%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	42.00%	6.70%	0.84%	50.42%	NA
Indica II	465	23.00%	46.50%	0.65%	29.89%	NA
Indica III	913	33.80%	36.40%	1.10%	28.70%	NA
Indica Intermediate	786	34.50%	30.70%	1.78%	33.08%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	66.70%	17.80%	0.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114587216	G -> A	LOC_Os01g25740.1	3_prime_UTR_variant ; 333.0bp to feature; MODIFIER	silent_mutation	Average:60.201; most accessible tissue: Callus, score: 73.987	N	N	N	N
vg0114587216	G -> A	LOC_Os01g25730.1	downstream_gene_variant ; 3838.0bp to feature; MODIFIER	silent_mutation	Average:60.201; most accessible tissue: Callus, score: 73.987	N	N	N	N
vg0114587216	G -> DEL	N	N	silent_mutation	Average:60.201; most accessible tissue: Callus, score: 73.987	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114587216	NA	2.40E-06	mr1428_2	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
vg0114587216	NA	3.49E-06	mr1654_2	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