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Detailed information for vg1109529032:

Variant ID: vg1109529032 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9529032
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: 72. )

Flanking Sequence (100 bp) in Reference Genome:

CCACGACGTCTGTCGAGGCCGCCGCAGGGGACGCGCTGGTAGTTGCCTCGGTCCCACCTTGCGCCGCCTTCACCCGCGCCGCCCTGCGAAGAGTTTCCTC[T/G]
TTCTCATAAAGCTAGGTGATCAAGAATTCGTGAATGGAAAAACTTCAAGAACGTCTACTTACTTATCGCCGATCGTCACCAGCCTTTGCCTCCGTTGAGG

Reverse complement sequence

CCTCAACGGAGGCAAAGGCTGGTGACGATCGGCGATAAGTAAGTAGACGTTCTTGAAGTTTTTCCATTCACGAATTCTTGATCACCTAGCTTTATGAGAA[A/C]
GAGGAAACTCTTCGCAGGGCGGCGCGGGTGAAGGCGGCGCAAGGTGGGACCGAGGCAACTACCAGCGCGTCCCCTGCGGCGGCCTCGACAGACGTCGTGG

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	35.40%	0.70%	28.80%	35.02%	NA
All Indica	2759	5.50%	1.10%	47.08%	46.28%	NA
All Japonica	1512	95.90%	0.00%	0.46%	3.64%	NA
Aus	269	4.10%	1.50%	15.24%	79.18%	NA
Indica I	595	9.70%	0.30%	27.56%	62.35%	NA
Indica II	465	4.10%	1.10%	57.42%	37.42%	NA
Indica III	913	2.10%	1.30%	56.30%	40.31%	NA
Indica Intermediate	786	7.30%	1.40%	45.04%	46.31%	NA
Temperate Japonica	767	97.30%	0.00%	0.13%	2.61%	NA
Tropical Japonica	504	94.20%	0.00%	0.79%	4.96%	NA
Japonica Intermediate	241	95.00%	0.00%	0.83%	4.15%	NA
VI/Aromatic	96	20.80%	0.00%	1.04%	78.12%	NA
Intermediate	90	45.60%	1.10%	14.44%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109529032	T -> DEL	N	N	silent_mutation	Average:22.145; most accessible tissue: Callus, score: 45.997	N	N	N	N
vg1109529032	T -> G	LOC_Os11g17150.1	downstream_gene_variant ; 3458.0bp to feature; MODIFIER	silent_mutation	Average:22.145; most accessible tissue: Callus, score: 45.997	N	N	N	N
vg1109529032	T -> G	LOC_Os11g17160.1	intron_variant ; MODIFIER	silent_mutation	Average:22.145; most accessible tissue: Callus, score: 45.997	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109529032	6.55E-06	NA	mr1639	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