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Detailed information for vg0124879589:

Variant ID: vg0124879589 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24879589
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, A: 0.33, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

ATACAATTTATATTAATTTATATTGTAGTTATAGTATACTTGTGGTGGAATTATATTACAACTATGTTACATTTAAAAGTTTGTCATTCAAAAAAAATTG[C/A]
GGCAATTTTTTTATAGTCCCTTTAAATAAAAAACACTAGAAACTTCGGTATGATTGCGGATTGAAAGATATGTCGCCAAGTATTCAAGTCAATGTGTACC

Reverse complement sequence

GGTACACATTGACTTGAATACTTGGCGACATATCTTTCAATCCGCAATCATACCGAAGTTTCTAGTGTTTTTTATTTAAAGGGACTATAAAAAAATTGCC[G/T]
CAATTTTTTTTGAATGACAAACTTTTAAATGTAACATAGTTGTAATATAATTCCACCACAAGTATACTATAACTACAATATAAATTAATATAAATTGTAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.10%	48.80%	1.12%	0.00%	NA
All Indica	2759	62.50%	35.70%	1.85%	0.00%	NA
All Japonica	1512	22.00%	77.90%	0.07%	0.00%	NA
Aus	269	94.10%	5.60%	0.37%	0.00%	NA
Indica I	595	48.90%	50.60%	0.50%	0.00%	NA
Indica II	465	48.60%	44.70%	6.67%	0.00%	NA
Indica III	913	72.40%	27.30%	0.33%	0.00%	NA
Indica Intermediate	786	69.50%	28.80%	1.78%	0.00%	NA
Temperate Japonica	767	1.60%	98.40%	0.00%	0.00%	NA
Tropical Japonica	504	56.50%	43.50%	0.00%	0.00%	NA
Japonica Intermediate	241	14.90%	84.60%	0.41%	0.00%	NA
VI/Aromatic	96	24.00%	76.00%	0.00%	0.00%	NA
Intermediate	90	37.80%	62.20%	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
vg0124879589	C -> A	LOC_Os01g43460-LOC_Os01g43470	intergenic_region ; MODIFIER	silent_mutation	Average:46.822; most accessible tissue: Callus, score: 70.297	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124879589	NA	1.03E-06	mr1090	Ind_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
vg0124879589	NA	9.42E-07	mr1211	Ind_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
vg0124879589	NA	3.63E-07	mr1227	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
vg0124879589	NA	2.93E-10	mr1633	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
vg0124879589	NA	1.20E-11	mr1921	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
vg0124879589	NA	9.84E-09	mr1068_2	Ind_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
vg0124879589	NA	1.98E-07	mr1078_2	Ind_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
vg0124879589	NA	5.50E-09	mr1090_2	Ind_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
vg0124879589	NA	1.70E-07	mr1121_2	Ind_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
vg0124879589	NA	1.49E-08	mr1211_2	Ind_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
vg0124879589	NA	6.74E-08	mr1244_2	Ind_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
vg0124879589	NA	2.13E-06	mr1545_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
vg0124879589	NA	1.49E-06	mr1951_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
vg0124879589	NA	1.19E-07	mr1951_2	Ind_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