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Detailed information for vg0912184179:

Variant ID: vg0912184179 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 12184179
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.69, A: 0.32, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

TATCAAGAGACCCCCAAGATCAATTTTTCCTTCCCCTTTCGCAACAAGCGTTTGATAAATATAAGGACATGCAAGAAAATCTCCATTCCTTTACCCTTCA[G/A]
GAGGTTGATGATTCATGGACATTCGTTTGGGGATCAGGGAAATTCACTTCGCGACTCTGTTACAAGCTCAGTTTTCTGGCTCTCACTCCCCCACCTACTA

Reverse complement sequence

TAGTAGGTGGGGGAGTGAGAGCCAGAAAACTGAGCTTGTAACAGAGTCGCGAAGTGAATTTCCCTGATCCCCAAACGAATGTCCATGAATCATCAACCTC[C/T]
TGAAGGGTAAAGGAATGGAGATTTTCTTGCATGTCCTTATATTTATCAAACGCTTGTTGCGAAAGGGGAAGGAAAAATTGATCTTGGGGGTCTCTTGATA

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	52.40%	46.80%	0.32%	0.44%	NA
All Indica	2759	26.80%	72.20%	0.40%	0.62%	NA
All Japonica	1512	98.40%	1.20%	0.26%	0.13%	NA
Aus	269	37.20%	62.80%	0.00%	0.00%	NA
Indica I	595	7.60%	91.60%	0.34%	0.50%	NA
Indica II	465	54.00%	45.20%	0.43%	0.43%	NA
Indica III	913	24.60%	74.70%	0.00%	0.66%	NA
Indica Intermediate	786	27.90%	70.50%	0.89%	0.76%	NA
Temperate Japonica	767	98.30%	1.30%	0.26%	0.13%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	96.70%	2.50%	0.41%	0.41%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	78.90%	18.90%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0912184179	G -> DEL	N	N	silent_mutation	Average:34.698; most accessible tissue: Callus, score: 54.158	N	N	N	N
vg0912184179	G -> A	LOC_Os09g20300.1	downstream_gene_variant ; 3814.0bp to feature; MODIFIER	silent_mutation	Average:34.698; most accessible tissue: Callus, score: 54.158	N	N	N	N
vg0912184179	G -> A	LOC_Os09g20300-LOC_Os09g20310	intergenic_region ; MODIFIER	silent_mutation	Average:34.698; most accessible tissue: Callus, score: 54.158	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0912184179	NA	9.25E-06	mr1397	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
vg0912184179	3.60E-06	1.90E-11	mr1425	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
vg0912184179	8.19E-06	4.62E-10	mr1425	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
vg0912184179	NA	4.70E-08	mr1439	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
vg0912184179	NA	4.01E-08	mr1660	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
vg0912184179	NA	3.72E-13	mr1667	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
vg0912184179	NA	7.92E-07	mr1796	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
vg0912184179	NA	5.29E-10	mr1986	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
vg0912184179	NA	8.91E-14	mr1717_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
vg0912184179	NA	9.71E-09	mr1895_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
vg0912184179	NA	8.57E-08	mr1895_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
vg0912184179	NA	1.25E-10	mr1946_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
vg0912184179	NA	7.06E-06	mr1946_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
vg0912184179	NA	1.25E-10	mr1948_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
vg0912184179	NA	7.06E-06	mr1948_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