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Detailed information for vg0826117244:

Variant ID: vg0826117244 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 26117244
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

CCTCCATATTTTAATGTTTTATAATTCGTCTTATTTAAAAAAATTATATAATTATTATTTATTTTATCATGACTTGATTCATCATCAAATATTCTTTAAG[C/T]
ATGACATAAATATTTTCATATTTGCATAAAAATTTTAAATAAAACAAATGGTCAAACACGTTGGTTGAAAAGTCAACGGCGTCAAACATTAAAATACGGA

Reverse complement sequence

TCCGTATTTTAATGTTTGACGCCGTTGACTTTTCAACCAACGTGTTTGACCATTTGTTTTATTTAAAATTTTTATGCAAATATGAAAATATTTATGTCAT[G/A]
CTTAAAGAATATTTGATGATGAATCAAGTCATGATAAAATAAATAATAATTATATAATTTTTTTAAATAAGACGAATTATAAAACATTAAAATATGGAGG

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	58.40%	39.20%	1.71%	0.70%	NA
All Indica	2759	31.80%	64.40%	2.65%	1.16%	NA
All Japonica	1512	97.70%	2.00%	0.33%	0.00%	NA
Aus	269	95.90%	4.10%	0.00%	0.00%	NA
Indica I	595	43.90%	51.90%	3.36%	0.84%	NA
Indica II	465	19.10%	71.60%	5.38%	3.87%	NA
Indica III	913	33.60%	65.90%	0.44%	0.00%	NA
Indica Intermediate	786	28.10%	67.70%	3.05%	1.15%	NA
Temperate Japonica	767	97.40%	2.20%	0.39%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	2.50%	0.83%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	60.00%	35.60%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0826117244	C -> T	LOC_Os08g41340.1	downstream_gene_variant ; 3330.0bp to feature; MODIFIER	silent_mutation	Average:60.01; most accessible tissue: Callus, score: 84.285	N	N	N	N
vg0826117244	C -> T	LOC_Os08g41320-LOC_Os08g41340	intergenic_region ; MODIFIER	silent_mutation	Average:60.01; most accessible tissue: Callus, score: 84.285	N	N	N	N
vg0826117244	C -> DEL	N	N	silent_mutation	Average:60.01; most accessible tissue: Callus, score: 84.285	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0826117244	NA	9.99E-06	mr1874	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
vg0826117244	NA	8.67E-09	mr1449_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
vg0826117244	2.10E-06	1.39E-09	mr1874_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