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Detailed information for vg0911050033:

Variant ID: vg0911050033 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11050033
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.02, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGACTCCGGTGGGCTCGTCCAACATCAGCAGGAGCTTGCCGTTGTTGATGCAGTCCAAGCAATGCTTCCCCTGCATCTCCCTGAAATGCTTTTCCATC[T/A]
AAGCTTCGGTCGGACATGTGGACAAAAGTTTGTGCTTGACTATGGTGTCCATGGCCTGCATCAGCCAAAGCCTAGTGCCAAAAGCCGCGGCAGCGATCAC

Reverse complement sequence

GTGATCGCTGCCGCGGCTTTTGGCACTAGGCTTTGGCTGATGCAGGCCATGGACACCATAGTCAAGCACAAACTTTTGTCCACATGTCCGACCGAAGCTT[A/T]
GATGGAAAAGCATTTCAGGGAGATGCAGGGGAAGCATTGCTTGGACTGCATCAACAACGGCAAGCTCCTGCTGATGTTGGACGAGCCCACCGGAGTCTTG

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	34.40%	11.70%	0.25%	53.70%	NA
All Indica	2759	8.60%	3.60%	0.36%	87.46%	NA
All Japonica	1512	84.00%	13.20%	0.07%	2.71%	NA
Aus	269	4.10%	77.30%	0.37%	18.22%	NA
Indica I	595	10.80%	3.20%	0.00%	86.05%	NA
Indica II	465	6.20%	6.70%	0.00%	87.10%	NA
Indica III	913	11.30%	1.20%	0.00%	87.51%	NA
Indica Intermediate	786	5.20%	4.80%	1.27%	88.68%	NA
Temperate Japonica	767	86.00%	13.00%	0.13%	0.78%	NA
Tropical Japonica	504	88.70%	5.40%	0.00%	5.95%	NA
Japonica Intermediate	241	67.60%	30.30%	0.00%	2.07%	NA
VI/Aromatic	96	51.00%	39.60%	0.00%	9.38%	NA
Intermediate	90	63.30%	7.80%	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
vg0911050033	T -> DEL	N	N	silent_mutation	Average:14.995; most accessible tissue: Callus, score: 63.653	N	N	N	N
vg0911050033	T -> A	LOC_Os09g18020-LOC_Os09g18040	intergenic_region ; MODIFIER	silent_mutation	Average:14.995; most accessible tissue: Callus, score: 63.653	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911050033	NA	1.31E-06	mr1210	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
vg0911050033	NA	4.07E-07	mr1305	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
vg0911050033	9.80E-07	5.35E-08	mr1585	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
vg0911050033	NA	1.19E-08	mr1586	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
vg0911050033	NA	6.48E-10	mr1927	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
vg0911050033	NA	1.84E-13	mr1807_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