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Detailed information for vg0139878087:

Variant ID: vg0139878087 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 39878087
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTAATTACACTGTAAGTATAGAATAATTACACTATAACTTATATGTAATTATACTGTAACTATAGTATAACTACACTGTAACTTTAGTATAACTACACT[G/A]
TAACTATAATAATTACATTGTTACTTATATGTAATTACATTGTAACTATAATATAACTTGCATGTAAGTGAGATGTACCTTTATAAAACTTATGTTTGGC

Reverse complement sequence

GCCAAACATAAGTTTTATAAAGGTACATCTCACTTACATGCAAGTTATATTATAGTTACAATGTAATTACATATAAGTAACAATGTAATTATTATAGTTA[C/T]
AGTGTAGTTATACTAAAGTTACAGTGTAGTTATACTATAGTTACAGTATAATTACATATAAGTTATAGTGTAATTATTCTATACTTACAGTGTAATTACA

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	93.40%	6.30%	0.25%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	80.00%	19.20%	0.79%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	76.40%	22.20%	1.43%	0.00%	NA
Tropical Japonica	504	86.30%	13.50%	0.20%	0.00%	NA
Japonica Intermediate	241	78.00%	22.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0139878087	G -> A	LOC_Os01g68670.1	upstream_gene_variant ; 872.0bp to feature; MODIFIER	silent_mutation	Average:63.871; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg0139878087	G -> A	LOC_Os01g68660.1	downstream_gene_variant ; 844.0bp to feature; MODIFIER	silent_mutation	Average:63.871; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg0139878087	G -> A	LOC_Os01g68680.1	downstream_gene_variant ; 2920.0bp to feature; MODIFIER	silent_mutation	Average:63.871; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg0139878087	G -> A	LOC_Os01g68660-LOC_Os01g68670	intergenic_region ; MODIFIER	silent_mutation	Average:63.871; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0139878087	NA	8.66E-06	mr1177_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