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Detailed information for vg0139046810:

Variant ID: vg0139046810 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 39046810
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.06, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

ATAGTAGCAATTGCATGTTTGATTTCAATAGTAGCAATTGCATGTTTGGTTTGCTACCAAATTTTATTTGCAATAGTTCAAACTAAACACCACCCAATTT[G/A]
GTAGTGTCAAAATTTACCAATGTTTTGGCAGTAACAAAATTTTGGTAGGACAAAAATTGGCTCCAAACCAAATAAACCCTTAATTTGAATCCGACCCGAC

Reverse complement sequence

GTCGGGTCGGATTCAAATTAAGGGTTTATTTGGTTTGGAGCCAATTTTTGTCCTACCAAAATTTTGTTACTGCCAAAACATTGGTAAATTTTGACACTAC[C/T]
AAATTGGGTGGTGTTTAGTTTGAACTATTGCAAATAAAATTTGGTAGCAAACCAAACATGCAATTGCTACTATTGAAATCAAACATGCAATTGCTACTAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.30%	45.20%	1.50%	0.00%	NA
All Indica	2759	75.20%	24.30%	0.51%	0.00%	NA
All Japonica	1512	19.80%	76.70%	3.51%	0.00%	NA
Aus	269	36.40%	62.80%	0.74%	0.00%	NA
Indica I	595	44.70%	54.60%	0.67%	0.00%	NA
Indica II	465	95.70%	4.10%	0.22%	0.00%	NA
Indica III	913	86.60%	12.90%	0.44%	0.00%	NA
Indica Intermediate	786	72.90%	26.50%	0.64%	0.00%	NA
Temperate Japonica	767	10.70%	84.50%	4.82%	0.00%	NA
Tropical Japonica	504	29.00%	69.60%	1.39%	0.00%	NA
Japonica Intermediate	241	29.90%	66.40%	3.73%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	42.20%	55.60%	2.22%	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
vg0139046810	G -> A	LOC_Os01g67260.1	upstream_gene_variant ; 4688.0bp to feature; MODIFIER	silent_mutation	Average:69.335; most accessible tissue: Callus, score: 97.38	N	N	N	N
vg0139046810	G -> A	LOC_Os01g67270.1	upstream_gene_variant ; 332.0bp to feature; MODIFIER	silent_mutation	Average:69.335; most accessible tissue: Callus, score: 97.38	N	N	N	N
vg0139046810	G -> A	LOC_Os01g67280.1	downstream_gene_variant ; 3030.0bp to feature; MODIFIER	silent_mutation	Average:69.335; most accessible tissue: Callus, score: 97.38	N	N	N	N
vg0139046810	G -> A	LOC_Os01g67260-LOC_Os01g67270	intergenic_region ; MODIFIER	silent_mutation	Average:69.335; most accessible tissue: Callus, score: 97.38	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0139046810	5.76E-06	2.53E-08	mr1522	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
vg0139046810	NA	1.86E-06	mr1583	Jap_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