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Detailed information for vg0817465290:

Variant ID: vg0817465290 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17465290
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATCTATTTATCTATTTCTATTATATACTAAAAGTCCATGAAACTTCCTACAAACGCTCCTAAGCCGCCATGTGTACTCCTACAAATACTCCTATACCGC[C/T]
ACATGTCATCTTAACAAATCGGTGGACCCAATATTTTTATCTATTAGAATTTTATTAAAAAAATAACCCCACAAACTCCCCTCCTCTCTCCTCTCCCCAT

Reverse complement sequence

ATGGGGAGAGGAGAGAGGAGGGGAGTTTGTGGGGTTATTTTTTTAATAAAATTCTAATAGATAAAAATATTGGGTCCACCGATTTGTTAAGATGACATGT[G/A]
GCGGTATAGGAGTATTTGTAGGAGTACACATGGCGGCTTAGGAGCGTTTGTAGGAAGTTTCATGGACTTTTAGTATATAATAGAAATAGATAAATAGATA

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	51.00%	2.70%	1.31%	44.99%	NA
All Indica	2759	30.20%	4.20%	1.67%	63.90%	NA
All Japonica	1512	82.90%	0.50%	0.93%	15.61%	NA
Aus	269	66.20%	0.00%	0.37%	33.46%	NA
Indica I	595	54.10%	1.50%	3.36%	41.01%	NA
Indica II	465	19.60%	0.60%	3.01%	76.77%	NA
Indica III	913	17.10%	11.10%	0.11%	71.74%	NA
Indica Intermediate	786	33.60%	0.50%	1.40%	64.50%	NA
Temperate Japonica	767	92.70%	0.80%	1.17%	5.35%	NA
Tropical Japonica	504	65.50%	0.20%	0.79%	33.53%	NA
Japonica Intermediate	241	88.40%	0.40%	0.41%	10.79%	NA
VI/Aromatic	96	88.50%	0.00%	0.00%	11.46%	NA
Intermediate	90	68.90%	1.10%	1.11%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817465290	C -> T	LOC_Os08g28590.1	downstream_gene_variant ; 3887.0bp to feature; MODIFIER	silent_mutation	Average:23.74; most accessible tissue: Callus, score: 90.217	N	N	N	N
vg0817465290	C -> T	LOC_Os08g28590-LOC_Os08g28600	intergenic_region ; MODIFIER	silent_mutation	Average:23.74; most accessible tissue: Callus, score: 90.217	N	N	N	N
vg0817465290	C -> DEL	N	N	silent_mutation	Average:23.74; most accessible tissue: Callus, score: 90.217	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817465290	NA	4.95E-06	mr1558_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