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Detailed information for vg1125145452:

Variant ID: vg1125145452 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25145452
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, G: 0.06, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTACATCTTTCTAAGAGATGTAAAACAGCAACTCAATAGAATTATTGAAATGTACTCAGGGTTTTTATTACAGGTGACAAAAAAGAATATGAGAGTAG[T/G]
GGTAATCGGGATTTATCAGAATTATATCGCCATAGACAAAATAAGCAAAATTTGAAAAAAAAAATTGGACAAAATTATGTATTACACCTACCCCTGTTGC

Reverse complement sequence

GCAACAGGGGTAGGTGTAATACATAATTTTGTCCAATTTTTTTTTTCAAATTTTGCTTATTTTGTCTATGGCGATATAATTCTGATAAATCCCGATTACC[A/C]
CTACTCTCATATTCTTTTTTGTCACCTGTAATAAAAACCCTGAGTACATTTCAATAATTCTATTGAGTTGCTGTTTTACATCTCTTAGAAAGATGTACTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.90%	34.90%	0.17%	0.00%	NA
All Indica	2759	52.20%	47.60%	0.29%	0.00%	NA
All Japonica	1512	86.50%	13.50%	0.00%	0.00%	NA
Aus	269	56.50%	43.50%	0.00%	0.00%	NA
Indica I	595	63.00%	36.60%	0.34%	0.00%	NA
Indica II	465	76.10%	23.90%	0.00%	0.00%	NA
Indica III	913	29.70%	70.30%	0.00%	0.00%	NA
Indica Intermediate	786	55.90%	43.40%	0.76%	0.00%	NA
Temperate Japonica	767	97.80%	2.20%	0.00%	0.00%	NA
Tropical Japonica	504	70.00%	30.00%	0.00%	0.00%	NA
Japonica Intermediate	241	85.10%	14.90%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	82.20%	17.80%	0.00%	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
vg1125145452	T -> G	LOC_Os11g41820.1	downstream_gene_variant ; 3251.0bp to feature; MODIFIER	silent_mutation	Average:39.264; most accessible tissue: Callus, score: 79.395	N	N	N	N
vg1125145452	T -> G	LOC_Os11g41820.2	downstream_gene_variant ; 3251.0bp to feature; MODIFIER	silent_mutation	Average:39.264; most accessible tissue: Callus, score: 79.395	N	N	N	N
vg1125145452	T -> G	LOC_Os11g41800-LOC_Os11g41820	intergenic_region ; MODIFIER	silent_mutation	Average:39.264; most accessible tissue: Callus, score: 79.395	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125145452	1.70E-08	3.78E-21	mr1133	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
vg1125145452	1.54E-07	4.52E-12	mr1133	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
vg1125145452	NA	6.47E-06	mr1925	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
vg1125145452	3.19E-06	2.07E-16	mr1133_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
vg1125145452	NA	1.00E-09	mr1133_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
vg1125145452	NA	6.62E-11	mr1667_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
vg1125145452	NA	9.17E-07	mr1667_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