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Detailed information for vg1126331556:

Variant ID: vg1126331556 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26331556
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, A: 0.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTGGGACGTAGTATTTGAAAAACACAAAAATGGGATAAATGCACGAATATGATGTCATGCATTATTGCATCCCAAAGGAAAAAAGTCCAGAGGCATTT[G/A]
CAAAACATTTTTTTAACCCGATAGGAAAAAACATAGGAATTCTAGAGACAACTAGGGGAAACCATGAGTTAAGACCTAATGTTAGTTTTCCTCCAAAACA

Reverse complement sequence

TGTTTTGGAGGAAAACTAACATTAGGTCTTAACTCATGGTTTCCCCTAGTTGTCTCTAGAATTCCTATGTTTTTTCCTATCGGGTTAAAAAAATGTTTTG[C/T]
AAATGCCTCTGGACTTTTTTCCTTTGGGATGCAATAATGCATGACATCATATTCGTGCATTTATCCCATTTTTGTGTTTTTCAAATACTACGTCCCAAAG

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	80.20%	19.70%	0.04%	0.00%	NA
All Indica	2759	72.10%	27.80%	0.07%	0.00%	NA
All Japonica	1512	98.30%	1.70%	0.00%	0.00%	NA
Aus	269	53.50%	46.50%	0.00%	0.00%	NA
Indica I	595	38.50%	61.50%	0.00%	0.00%	NA
Indica II	465	83.20%	16.80%	0.00%	0.00%	NA
Indica III	913	76.80%	23.10%	0.11%	0.00%	NA
Indica Intermediate	786	85.60%	14.20%	0.13%	0.00%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	95.00%	5.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	15.60%	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
vg1126331556	G -> A	LOC_Os11g43650.1	downstream_gene_variant ; 1099.0bp to feature; MODIFIER	silent_mutation	Average:29.868; most accessible tissue: Callus, score: 61.627	N	N	N	N
vg1126331556	G -> A	LOC_Os11g43650-LOC_Os11g43660	intergenic_region ; MODIFIER	silent_mutation	Average:29.868; most accessible tissue: Callus, score: 61.627	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126331556	7.89E-09	7.94E-15	mr1191	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
vg1126331556	9.30E-10	7.42E-11	mr1191	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
vg1126331556	4.79E-09	1.23E-15	mr1644	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
vg1126331556	4.92E-09	3.24E-11	mr1644	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
vg1126331556	NA	4.77E-12	mr1662	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
vg1126331556	NA	3.27E-10	mr1662	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
vg1126331556	2.45E-08	4.35E-22	mr1191_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
vg1126331556	5.58E-08	2.74E-14	mr1191_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
vg1126331556	5.23E-06	9.47E-10	mr1530_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
vg1126331556	NA	5.60E-11	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
vg1126331556	5.18E-06	1.24E-12	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
vg1126331556	NA	1.05E-10	mr1745_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