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Detailed information for vg0911047829:

Variant ID: vg0911047829 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11047829
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.05, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

TGCTGTTTCATTATTTCAAACTCAATCGCATATATGCAGCTATATGGGCTATGGTTTTAAGTAGGTGAATATCTCATTGGTGGACATACTCTTGCTTCAA[T/A]
CTTTCTTTGTGGTATAGCATTTGAGAAACATCAATTCTAATGTTGGTTAAGTGTATAATTGAAGAACTAGCATACCTTCAGGTTTCATGAAACATTACTG

Reverse complement sequence

CAGTAATGTTTCATGAAACCTGAAGGTATGCTAGTTCTTCAATTATACACTTAACCAACATTAGAATTGATGTTTCTCAAATGCTATACCACAAAGAAAG[A/T]
TTGAAGCAAGAGTATGTCCACCAATGAGATATTCACCTACTTAAAACCATAGCCCATATAGCTGCATATATGCGATTGAGTTTGAAATAATGAAACAGCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.50%	12.80%	0.59%	53.13%	NA
All Indica	2759	8.60%	3.70%	0.87%	86.81%	NA
All Japonica	1512	84.10%	13.30%	0.07%	2.58%	NA
Aus	269	6.30%	77.00%	1.12%	15.61%	NA
Indica I	595	11.30%	3.20%	1.01%	84.54%	NA
Indica II	465	5.80%	6.70%	1.08%	86.45%	NA
Indica III	913	10.80%	1.40%	0.44%	87.29%	NA
Indica Intermediate	786	5.70%	5.00%	1.15%	88.17%	NA
Temperate Japonica	767	86.20%	13.00%	0.00%	0.78%	NA
Tropical Japonica	504	88.90%	5.40%	0.20%	5.56%	NA
Japonica Intermediate	241	67.20%	30.70%	0.00%	2.07%	NA
VI/Aromatic	96	9.40%	81.20%	0.00%	9.38%	NA
Intermediate	90	52.20%	18.90%	0.00%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0911047829	T -> DEL	N	N	silent_mutation	Average:7.755; most accessible tissue: Callus, score: 30.511	N	N	N	N
vg0911047829	T -> A	LOC_Os09g18020-LOC_Os09g18040	intergenic_region ; MODIFIER	silent_mutation	Average:7.755; most accessible tissue: Callus, score: 30.511	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911047829	NA	1.09E-11	mr1409	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
vg0911047829	NA	5.86E-12	mr1585	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
vg0911047829	NA	4.74E-08	mr1585_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
vg0911047829	1.22E-06	6.94E-06	mr1768_2	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