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Detailed information for vg0808861923:

Variant ID: vg0808861923 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8861923
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTTTTCCCAGATTTGAACTTTATAAAACAGCAAAACTGAACTTTATATACCATGTATTCTTTGAGTGCCATTTATCTAAATTTCTTTGGAGAGCTATA[C/T]
AATTCTCTTTTGGACTTTATCCTCCATATAGTATATCTCATATGTTTGGAAATTGGCTTGTGGTTGTTAGTAAAAAAATAAAAAAAACTTATTCTTTTTG

Reverse complement sequence

CAAAAAGAATAAGTTTTTTTTATTTTTTTACTAACAACCACAAGCCAATTTCCAAACATATGAGATATACTATATGGAGGATAAAGTCCAAAAGAGAATT[G/A]
TATAGCTCTCCAAAGAAATTTAGATAAATGGCACTCAAAGAATACATGGTATATAAAGTTCAGTTTTGCTGTTTTATAAAGTTCAAATCTGGGAAAAAAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.50%	32.30%	0.17%	0.00%	NA
All Indica	2759	57.30%	42.40%	0.29%	0.00%	NA
All Japonica	1512	88.90%	11.10%	0.00%	0.00%	NA
Aus	269	40.10%	59.90%	0.00%	0.00%	NA
Indica I	595	60.80%	38.70%	0.50%	0.00%	NA
Indica II	465	84.10%	15.90%	0.00%	0.00%	NA
Indica III	913	40.20%	59.50%	0.33%	0.00%	NA
Indica Intermediate	786	58.50%	41.20%	0.25%	0.00%	NA
Temperate Japonica	767	98.40%	1.60%	0.00%	0.00%	NA
Tropical Japonica	504	78.00%	22.00%	0.00%	0.00%	NA
Japonica Intermediate	241	81.30%	18.70%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	77.80%	22.20%	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
vg0808861923	C -> T	LOC_Os08g14730.1	downstream_gene_variant ; 566.0bp to feature; MODIFIER	silent_mutation	Average:73.444; most accessible tissue: Callus, score: 85.559	N	N	N	N
vg0808861923	C -> T	LOC_Os08g14720-LOC_Os08g14730	intergenic_region ; MODIFIER	silent_mutation	Average:73.444; most accessible tissue: Callus, score: 85.559	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808861923	NA	3.27E-06	mr1042	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
vg0808861923	NA	1.61E-09	mr1059	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
vg0808861923	6.81E-07	NA	mr1566_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