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Detailed information for vg0819535183:

Variant ID: vg0819535183 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19535183
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

CTAATTTAGAGTATTAAATATAGACTACTTACAAAACTAATTATATAAATGAAAGCTAATTCGCGAGACAAATTTTTTAAGCCTAATTAATCCATAATTA[G/A]
ATAATGTTTACTGTAGCATCATATAGGCTAATCATGGATTAATTAGGCTCAATAGATTCGTCTCGCGAATTAGTCCAAGATTATGGATGGGTTTTATTAA

Reverse complement sequence

TTAATAAAACCCATCCATAATCTTGGACTAATTCGCGAGACGAATCTATTGAGCCTAATTAATCCATGATTAGCCTATATGATGCTACAGTAAACATTAT[C/T]
TAATTATGGATTAATTAGGCTTAAAAAATTTGTCTCGCGAATTAGCTTTCATTTATATAATTAGTTTTGTAAGTAGTCTATATTTAATACTCTAAATTAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.10%	5.90%	0.00%	0.00%	NA
All Indica	2759	97.40%	2.60%	0.00%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	44.60%	55.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	98.20%	1.80%	0.00%	0.00%	NA
Indica Intermediate	786	94.10%	5.90%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	56.20%	43.80%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg0819535183	G -> A	LOC_Os08g31569.1	upstream_gene_variant ; 2034.0bp to feature; MODIFIER	silent_mutation	Average:41.545; most accessible tissue: Callus, score: 65.761	N	N	N	N
vg0819535183	G -> A	LOC_Os08g31569-LOC_Os08g31580	intergenic_region ; MODIFIER	silent_mutation	Average:41.545; most accessible tissue: Callus, score: 65.761	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819535183	NA	8.00E-06	mr1230_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
vg0819535183	3.47E-06	1.54E-08	mr1930_2	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