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Detailed information for vg1126565937:

Variant ID: vg1126565937 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26565937
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.74, C: 0.27, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCTATCTCTTCTCTATCTTATATCTCCATCTCTATCTCTACTATTATAAAAATTGAAAATATTTTTGCCGGTACTTTGATACGTTATTCATGCATGAG[T/C]
CAGTTCTTAAGTTCGTTTGATTTTGGAATTATGGTTCCGTATTTGAGTCGGGCTTTAAGTTCGTTCGCTTTTCAAAATACAAAAGGAGTCATATAAGATA

Reverse complement sequence

TATCTTATATGACTCCTTTTGTATTTTGAAAAGCGAACGAACTTAAAGCCCGACTCAAATACGGAACCATAATTCCAAAATCAAACGAACTTAAGAACTG[A/G]
CTCATGCATGAATAACGTATCAAAGTACCGGCAAAAATATTTTCAATTTTTATAATAGTAGAGATAGAGATGGAGATATAAGATAGAGAAGAGATAGAGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.70%	27.20%	0.13%	0.00%	NA
All Indica	2759	59.00%	40.80%	0.18%	0.00%	NA
All Japonica	1512	95.60%	4.40%	0.00%	0.00%	NA
Aus	269	75.80%	24.20%	0.00%	0.00%	NA
Indica I	595	87.20%	12.80%	0.00%	0.00%	NA
Indica II	465	82.40%	17.60%	0.00%	0.00%	NA
Indica III	913	26.60%	73.20%	0.22%	0.00%	NA
Indica Intermediate	786	61.50%	38.20%	0.38%	0.00%	NA
Temperate Japonica	767	96.10%	3.90%	0.00%	0.00%	NA
Tropical Japonica	504	94.80%	5.20%	0.00%	0.00%	NA
Japonica Intermediate	241	95.40%	4.60%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	77.80%	21.10%	1.11%	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
vg1126565937	T -> C	LOC_Os11g43970.1	upstream_gene_variant ; 2596.0bp to feature; MODIFIER	silent_mutation	Average:73.536; most accessible tissue: Minghui63 root, score: 91.96	N	N	N	N
vg1126565937	T -> C	LOC_Os11g43970-LOC_Os11g43980	intergenic_region ; MODIFIER	silent_mutation	Average:73.536; most accessible tissue: Minghui63 root, score: 91.96	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126565937	NA	5.74E-11	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
vg1126565937	NA	7.27E-06	mr1538	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
vg1126565937	NA	4.99E-07	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
vg1126565937	NA	2.59E-08	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
vg1126565937	NA	7.08E-08	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
vg1126565937	NA	3.60E-06	mr1980	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
vg1126565937	NA	6.47E-12	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
vg1126565937	8.86E-06	2.10E-09	mr1517_2	Jap_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
vg1126565937	NA	2.16E-09	mr1538_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
vg1126565937	NA	1.83E-06	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
vg1126565937	NA	2.67E-07	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
vg1126565937	NA	1.65E-08	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