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Detailed information for vg0819608857:

Variant ID: vg0819608857 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19608857
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCGTTCTGCAATATAAGGGATTTTGAGTTTTTGTTTGCAACGTTTGACCACTCGTCTTATTTAAATTCTTTTTCCAAATATAAAAAACAAAAAGTTGT[G/T]
CTTAAAGTACTGTAGATAATAAAGTAAGTCACAAATAAAATAAATAATAATTTCAAAAAATTTTAAATATGATGAGTGGTCAAACGTTACAAGCAAAAAC

Reverse complement sequence

GTTTTTGCTTGTAACGTTTGACCACTCATCATATTTAAAATTTTTTGAAATTATTATTTATTTTATTTGTGACTTACTTTATTATCTACAGTACTTTAAG[C/A]
ACAACTTTTTGTTTTTTATATTTGGAAAAAGAATTTAAATAAGACGAGTGGTCAAACGTTGCAAACAAAAACTCAAAATCCCTTATATTGCAGAACGGAG

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	94.30%	5.70%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	82.40%	17.60%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	83.10%	16.90%	0.00%	0.00%	NA
Tropical Japonica	504	96.80%	3.20%	0.00%	0.00%	NA
Japonica Intermediate	241	50.20%	49.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0819608857	G -> T	LOC_Os08g31660.1	upstream_gene_variant ; 1587.0bp to feature; MODIFIER	silent_mutation	Average:53.448; most accessible tissue: Minghui63 root, score: 87.964	N	N	N	N
vg0819608857	G -> T	LOC_Os08g31649-LOC_Os08g31660	intergenic_region ; MODIFIER	silent_mutation	Average:53.448; most accessible tissue: Minghui63 root, score: 87.964	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819608857	4.46E-06	NA	mr1858	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
vg0819608857	4.37E-06	NA	mr1859	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
vg0819608857	8.22E-06	NA	mr1310_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