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Detailed information for vg0817489232:

Variant ID: vg0817489232 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17489232
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTTAGAGATAAGAGTCGTCTCCGACATGGACATATTTTGTAATCTCGGGTATAAATAGACCCCGAGCACCATGTAATCAGATAACACACATTCAATAAC[A/T]
ATCTCAGCGCATCGCCACCCTTTTACTTTCGTTTTGTTTTCGACGAGTTCTTGCTTTTGGGTTGAGCTGCATCGGTTTCAATCTTCAACTAGAGGTAAAA

Reverse complement sequence

TTTTACCTCTAGTTGAAGATTGAAACCGATGCAGCTCAACCCAAAAGCAAGAACTCGTCGAAAACAAAACGAAAGTAAAAGGGTGGCGATGCGCTGAGAT[T/A]
GTTATTGAATGTGTGTTATCTGATTACATGGTGCTCGGGGTCTATTTATACCCGAGATTACAAAATATGTCCATGTCGGAGACGACTCTTATCTCTAACA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.50%	1.60%	9.10%	36.80%	NA
All Indica	2759	35.80%	0.00%	10.08%	54.08%	NA
All Japonica	1512	77.10%	5.00%	8.27%	9.66%	NA
Aus	269	65.80%	0.00%	7.81%	26.39%	NA
Indica I	595	57.60%	0.00%	12.77%	29.58%	NA
Indica II	465	23.70%	0.20%	9.46%	66.67%	NA
Indica III	913	30.60%	0.00%	7.45%	61.99%	NA
Indica Intermediate	786	32.60%	0.00%	11.45%	55.98%	NA
Temperate Japonica	767	84.10%	8.30%	6.39%	1.17%	NA
Tropical Japonica	504	65.50%	0.00%	10.52%	24.01%	NA
Japonica Intermediate	241	78.80%	5.00%	9.54%	6.64%	NA
VI/Aromatic	96	89.60%	0.00%	0.00%	10.42%	NA
Intermediate	90	71.10%	0.00%	6.67%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817489232	A -> T	LOC_Os08g28620.1	upstream_gene_variant ; 1713.0bp to feature; MODIFIER	silent_mutation	Average:9.881; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N
vg0817489232	A -> T	LOC_Os08g28630.1	upstream_gene_variant ; 1375.0bp to feature; MODIFIER	silent_mutation	Average:9.881; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N
vg0817489232	A -> T	LOC_Os08g28620-LOC_Os08g28630	intergenic_region ; MODIFIER	silent_mutation	Average:9.881; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N
vg0817489232	A -> DEL	N	N	silent_mutation	Average:9.881; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817489232	3.02E-07	3.02E-07	mr1806	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