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Detailed information for vg0818033565:

Variant ID: vg0818033565 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18033565
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGGATCGTCGTTGAACCGTCAACGACGACCCTATTGATGTTGACGACCTGCATGGTTAATTTATTCGTAAATATTCGTAACATTTGACGAAGAGAAAG[G/T]
AATAAAAGATAAAGGAATGGTGCGATGCAGGGTACTCACAGCACGAGCGAAGTCCTGGTCGCGGTGCCTGGCGTAGAGGTCTCTAGTGCTCGCAACGTGG

Reverse complement sequence

CCACGTTGCGAGCACTAGAGACCTCTACGCCAGGCACCGCGACCAGGACTTCGCTCGTGCTGTGAGTACCCTGCATCGCACCATTCCTTTATCTTTTATT[C/A]
CTTTCTCTTCGTCAAATGTTACGAATATTTACGAATAAATTAACCATGCAGGTCGTCAACATCAATAGGGTCGTCGTTGACGGTTCAACGACGATCCAAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.60%	7.40%	0.02%	0.00%	NA
All Indica	2759	97.30%	2.70%	0.04%	0.00%	NA
All Japonica	1512	84.50%	15.50%	0.00%	0.00%	NA
Aus	269	91.40%	8.60%	0.00%	0.00%	NA
Indica I	595	96.10%	3.90%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	98.10%	1.90%	0.00%	0.00%	NA
Indica Intermediate	786	96.10%	3.80%	0.13%	0.00%	NA
Temperate Japonica	767	98.40%	1.60%	0.00%	0.00%	NA
Tropical Japonica	504	60.50%	39.50%	0.00%	0.00%	NA
Japonica Intermediate	241	90.50%	9.50%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	0.00%	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
vg0818033565	G -> T	LOC_Os08g29400.1	downstream_gene_variant ; 2180.0bp to feature; MODIFIER	silent_mutation	Average:50.288; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N
vg0818033565	G -> T	LOC_Os08g29420.1	downstream_gene_variant ; 2716.0bp to feature; MODIFIER	silent_mutation	Average:50.288; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N
vg0818033565	G -> T	LOC_Os08g29400.2	downstream_gene_variant ; 2180.0bp to feature; MODIFIER	silent_mutation	Average:50.288; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N
vg0818033565	G -> T	LOC_Os08g29400-LOC_Os08g29420	intergenic_region ; MODIFIER	silent_mutation	Average:50.288; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818033565	4.30E-06	2.41E-06	mr1836	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
vg0818033565	3.69E-06	3.00E-08	mr1836_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