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Detailed information for vg1218863509:

Variant ID: vg1218863509 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18863509
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.75, G: 0.23, others allele: 0.00, population size: 159. )

Flanking Sequence (100 bp) in Reference Genome:

CTTGTGCTTTTGCCATTTATATTGAGCTCCACCTTGCTAGTAATAAATTACTATACCTATTGTTTTTCTATTTAACATGACATGAATGAATGAACAAATA[G/A]
CCACATTAAAATAACATTATGTTAACAGGGGCATGTGCTCCCATTCTTTTCTCTCCATTAAATATTATTGGGTCATAAGGGGCAATATGCCCCCTCTAAT

Reverse complement sequence

ATTAGAGGGGGCATATTGCCCCTTATGACCCAATAATATTTAATGGAGAGAAAAGAATGGGAGCACATGCCCCTGTTAACATAATGTTATTTTAATGTGG[C/T]
TATTTGTTCATTCATTCATGTCATGTTAAATAGAAAAACAATAGGTATAGTAATTTATTACTAGCAAGGTGGAGCTCAATATAAATGGCAAAAGCACAAG

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	61.30%	38.50%	0.21%	0.00%	NA
All Indica	2759	90.60%	9.30%	0.11%	0.00%	NA
All Japonica	1512	7.20%	92.50%	0.26%	0.00%	NA
Aus	269	88.50%	11.50%	0.00%	0.00%	NA
Indica I	595	95.60%	4.40%	0.00%	0.00%	NA
Indica II	465	78.30%	21.70%	0.00%	0.00%	NA
Indica III	913	94.70%	5.10%	0.11%	0.00%	NA
Indica Intermediate	786	89.20%	10.60%	0.25%	0.00%	NA
Temperate Japonica	767	2.00%	97.90%	0.13%	0.00%	NA
Tropical Japonica	504	5.80%	94.00%	0.20%	0.00%	NA
Japonica Intermediate	241	27.00%	72.20%	0.83%	0.00%	NA
VI/Aromatic	96	21.90%	78.10%	0.00%	0.00%	NA
Intermediate	90	32.20%	64.40%	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
vg1218863509	G -> A	LOC_Os12g31350.1	upstream_gene_variant ; 2862.0bp to feature; MODIFIER	silent_mutation	Average:28.486; most accessible tissue: Callus, score: 78.828	N	N	N	N
vg1218863509	G -> A	LOC_Os12g31350-LOC_Os12g31370	intergenic_region ; MODIFIER	silent_mutation	Average:28.486; most accessible tissue: Callus, score: 78.828	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218863509	NA	2.78E-06	mr1118	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
vg1218863509	NA	2.58E-08	mr1242	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
vg1218863509	NA	4.11E-21	mr1254	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
vg1218863509	NA	3.03E-15	mr1361	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
vg1218863509	NA	2.73E-08	mr1442	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
vg1218863509	NA	7.80E-08	mr1458	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
vg1218863509	NA	1.85E-11	mr1553	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
vg1218863509	NA	1.08E-07	mr1646	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
vg1218863509	1.34E-06	1.34E-06	mr1750	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
vg1218863509	NA	9.35E-07	mr1797	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
vg1218863509	NA	9.35E-07	mr1801	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
vg1218863509	NA	1.77E-07	mr1835	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
vg1218863509	NA	1.83E-06	mr1944	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
vg1218863509	3.10E-08	3.10E-08	mr1987	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
vg1218863509	NA	8.53E-06	mr1457_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
vg1218863509	7.77E-06	NA	mr1458_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
vg1218863509	3.40E-08	2.99E-09	mr1458_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