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Detailed information for vg0135058442:

Variant ID: vg0135058442 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 35058442
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.88, G: 0.13, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTTAAGTCCCTATCACATCGGATGTTTGAACACTAATTATAAATATTAAATATAGACTATTAATAAAACCTATCCATAATCTTAGACTAATTCGCGAG[G/A]
CGAATCTATTGAGCCTAATTAATCCATGATTAGCCTATGTGATGCTACATTAAACATTCTCTAATTATGGATTAATTAGGCTTAAAAAATTTATCTCGCG

Reverse complement sequence

CGCGAGATAAATTTTTTAAGCCTAATTAATCCATAATTAGAGAATGTTTAATGTAGCATCACATAGGCTAATCATGGATTAATTAGGCTCAATAGATTCG[C/T]
CTCGCGAATTAGTCTAAGATTATGGATAGGTTTTATTAATAGTCTATATTTAATATTTATAATTAGTGTTCAAACATCCGATGTGATAGGGACTTAAAAT

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	65.90%	33.60%	0.44%	0.08%	NA
All Indica	2759	96.70%	2.60%	0.62%	0.14%	NA
All Japonica	1512	8.30%	91.60%	0.07%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	95.50%	3.90%	0.67%	0.00%	NA
Indica II	465	97.20%	1.50%	1.29%	0.00%	NA
Indica III	913	98.90%	0.40%	0.33%	0.33%	NA
Indica Intermediate	786	94.70%	4.70%	0.51%	0.13%	NA
Temperate Japonica	767	1.60%	98.40%	0.00%	0.00%	NA
Tropical Japonica	504	18.70%	81.30%	0.00%	0.00%	NA
Japonica Intermediate	241	8.30%	91.30%	0.41%	0.00%	NA
VI/Aromatic	96	10.40%	89.60%	0.00%	0.00%	NA
Intermediate	90	48.90%	47.80%	3.33%	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
vg0135058442	G -> A	LOC_Os01g60630.1	upstream_gene_variant ; 4856.0bp to feature; MODIFIER	silent_mutation	Average:40.316; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0135058442	G -> A	LOC_Os01g60640.1	upstream_gene_variant ; 4292.0bp to feature; MODIFIER	silent_mutation	Average:40.316; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0135058442	G -> A	LOC_Os01g60630-LOC_Os01g60640	intergenic_region ; MODIFIER	silent_mutation	Average:40.316; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0135058442	G -> DEL	N	N	silent_mutation	Average:40.316; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0135058442	NA	7.71E-102	mr1008	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
vg0135058442	NA	8.61E-24	mr1375	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
vg0135058442	NA	6.05E-07	mr1781	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
vg0135058442	2.75E-07	2.75E-07	mr1954_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