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Detailed information for vg0215574189:

Variant ID: vg0215574189 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 15574189
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: 277. )

Flanking Sequence (100 bp) in Reference Genome:

GCTAAAACCGATGTCCAAACCGTTATGGGACCTATATTGCATCGGTTTTGGTAGTTGAAGGACACGCTGTATCTGGTTTTCCGGTTGAAGGACGAAAGTC[G/A]
GATTTGTTGATAAGTTAAGGGACCTCAAGTGAATGTATTCCTTATTCAGCAGATTGCCGCTGCACAAAAGGAATAAGTTCACTTTGACTCCCTTAAAAGT

Reverse complement sequence

ACTTTTAAGGGAGTCAAAGTGAACTTATTCCTTTTGTGCAGCGGCAATCTGCTGAATAAGGAATACATTCACTTGAGGTCCCTTAACTTATCAACAAATC[C/T]
GACTTTCGTCCTTCAACCGGAAAACCAGATACAGCGTGTCCTTCAACTACCAAAACCGATGCAATATAGGTCCCATAACGGTTTGGACATCGGTTTTAGC

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	92.20%	6.70%	1.08%	0.00%	NA
All Indica	2759	87.00%	11.20%	1.74%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.00%	0.50%	0.00%	NA
Indica II	465	71.40%	24.10%	4.52%	0.00%	NA
Indica III	913	83.40%	15.90%	0.77%	0.00%	NA
Indica Intermediate	786	91.10%	6.70%	2.16%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	6.70%	3.33%	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
vg0215574189	G -> A	LOC_Os02g26520.1	upstream_gene_variant ; 782.0bp to feature; MODIFIER	silent_mutation	Average:48.735; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0215574189	G -> A	LOC_Os02g26530.1	upstream_gene_variant ; 346.0bp to feature; MODIFIER	silent_mutation	Average:48.735; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0215574189	G -> A	LOC_Os02g26540.1	downstream_gene_variant ; 2952.0bp to feature; MODIFIER	silent_mutation	Average:48.735; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0215574189	G -> A	LOC_Os02g26520-LOC_Os02g26530	intergenic_region ; MODIFIER	silent_mutation	Average:48.735; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0215574189	NA	1.22E-06	mr1129	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
vg0215574189	NA	6.77E-08	mr1130	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
vg0215574189	NA	5.03E-07	mr1317	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
vg0215574189	NA	9.35E-06	mr1818	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
vg0215574189	1.82E-06	NA	mr1855	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
vg0215574189	NA	8.30E-15	mr1855	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
vg0215574189	NA	6.65E-06	mr1050_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
vg0215574189	NA	9.44E-09	mr1317_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
vg0215574189	2.41E-08	NA	mr1855_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
vg0215574189	4.59E-07	5.21E-13	mr1855_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
vg0215574189	NA	1.39E-06	mr1897_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
vg0215574189	3.27E-07	NA	mr1914_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
vg0215574189	1.53E-06	1.37E-10	mr1914_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
vg0215574189	NA	1.60E-06	mr1927_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