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Detailed information for vg1125514201:

Variant ID: vg1125514201 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25514201
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TGCAGAGTTAGTGTACCTTCATTAATTAATTTGTTGATTAATACTAATTTTCCTTTTCTTCTTCTACTACTCCAGTATATATATATCATCATTTATATCT[T/G]
ACATGCCTGCCATTTGGCATTTCTTCTTATCAGACAGCAAGATATACCATGTCCAGAATATGGGCAAACAATGACACAGTAAGAGAGGCACTTGGAATAC

Reverse complement sequence

GTATTCCAAGTGCCTCTCTTACTGTGTCATTGTTTGCCCATATTCTGGACATGGTATATCTTGCTGTCTGATAAGAAGAAATGCCAAATGGCAGGCATGT[A/C]
AGATATAAATGATGATATATATATACTGGAGTAGTAGAAGAAGAAAAGGAAAATTAGTATTAATCAACAAATTAATTAATGAAGGTACACTAACTCTGCA

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	62.70%	35.90%	0.30%	1.08%	NA
All Indica	2759	46.10%	51.70%	0.40%	1.78%	NA
All Japonica	1512	87.20%	12.70%	0.00%	0.13%	NA
Aus	269	80.70%	18.20%	1.12%	0.00%	NA
Indica I	595	87.40%	12.60%	0.00%	0.00%	NA
Indica II	465	77.00%	22.40%	0.22%	0.43%	NA
Indica III	913	8.20%	87.80%	0.22%	3.72%	NA
Indica Intermediate	786	40.70%	56.60%	1.02%	1.65%	NA
Temperate Japonica	767	97.30%	2.50%	0.00%	0.26%	NA
Tropical Japonica	504	71.60%	28.40%	0.00%	0.00%	NA
Japonica Intermediate	241	87.60%	12.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	66.70%	33.30%	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
vg1125514201	T -> DEL	N	N	silent_mutation	Average:61.768; most accessible tissue: Callus, score: 81.916	N	N	N	N
vg1125514201	T -> G	LOC_Os11g42400.1	upstream_gene_variant ; 4957.0bp to feature; MODIFIER	silent_mutation	Average:61.768; most accessible tissue: Callus, score: 81.916	N	N	N	N
vg1125514201	T -> G	LOC_Os11g42390.1	intron_variant ; MODIFIER	silent_mutation	Average:61.768; most accessible tissue: Callus, score: 81.916	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125514201	NA	1.04E-09	Heading_date	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1125514201	NA	7.93E-08	mr1063	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
vg1125514201	4.58E-14	8.34E-32	mr1133	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
vg1125514201	9.12E-14	2.28E-25	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
vg1125514201	1.47E-06	1.47E-06	mr1540	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
vg1125514201	4.36E-17	9.20E-21	mr1662	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
vg1125514201	2.37E-10	1.03E-14	mr1662	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
vg1125514201	NA	2.36E-06	mr1662	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
vg1125514201	5.59E-10	7.96E-18	mr1667	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
vg1125514201	4.11E-10	9.31E-16	mr1667	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
vg1125514201	NA	1.94E-06	mr1732	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
vg1125514201	1.94E-14	1.42E-31	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
vg1125514201	3.95E-12	6.71E-25	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
vg1125514201	6.01E-14	1.77E-16	mr1662_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
vg1125514201	4.43E-08	1.39E-11	mr1662_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
vg1125514201	NA	3.57E-06	mr1662_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
vg1125514201	6.17E-10	9.47E-19	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
vg1125514201	5.11E-10	8.43E-17	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