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Detailed information for vg0904740928:

Variant ID: vg0904740928 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 4740928
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: 107. )

Flanking Sequence (100 bp) in Reference Genome:

ATATATTTATCGAGGGATATTTGACACCAAGTTGATCCATTTTATCATGTGAAATTATTTAAAAAATTATCATGACATTATGACATTAATTATTATATGT[T/G]
GGCTAAATTATTTAAAAATAATTATGACATTAAGTATTATATGACGGCACCATGTATTTAGCACTACAATATAACTATTATATGTGATCAATATTTTATT

Reverse complement sequence

AATAAAATATTGATCACATATAATAGTTATATTGTAGTGCTAAATACATGGTGCCGTCATATAATACTTAATGTCATAATTATTTTTAAATAATTTAGCC[A/C]
ACATATAATAATTAATGTCATAATGTCATGATAATTTTTTAAATAATTTCACATGATAAAATGGATCAACTTGGTGTCAAATATCCCTCGATAAATATAT

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	50.60%	3.60%	21.37%	24.40%	NA
All Indica	2759	41.10%	6.20%	34.07%	18.63%	NA
All Japonica	1512	64.70%	0.00%	1.79%	33.47%	NA
Aus	269	83.30%	0.00%	5.20%	11.52%	NA
Indica I	595	36.30%	8.70%	34.62%	20.34%	NA
Indica II	465	41.70%	2.80%	37.63%	17.85%	NA
Indica III	913	42.10%	7.20%	31.65%	19.06%	NA
Indica Intermediate	786	43.30%	5.10%	34.35%	17.30%	NA
Temperate Japonica	767	97.70%	0.00%	0.39%	1.96%	NA
Tropical Japonica	504	21.20%	0.00%	3.57%	75.20%	NA
Japonica Intermediate	241	51.00%	0.00%	2.49%	46.47%	NA
VI/Aromatic	96	20.80%	0.00%	6.25%	72.92%	NA
Intermediate	90	38.90%	0.00%	25.56%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0904740928	T -> G	LOC_Os09g08920.1	upstream_gene_variant ; 3088.0bp to feature; MODIFIER	silent_mutation	Average:18.382; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0904740928	T -> G	LOC_Os09g08920-LOC_Os09g08930	intergenic_region ; MODIFIER	silent_mutation	Average:18.382; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0904740928	T -> DEL	N	N	silent_mutation	Average:18.382; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0904740928	2.70E-07	NA	mr1865	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
vg0904740928	6.97E-08	1.72E-10	mr1865	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
vg0904740928	6.36E-06	6.11E-10	mr1865_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