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Detailed information for vg1219745087:

Variant ID: vg1219745087 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19745087
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:

CCGACAGCCACACCTACAAGCTACAGCTGAAGCATCAGATAGGGCAGAGGAGGCATCACAGGTCTGGTTTGGATTAAATTTAATGTTGCACTTTGTATAG[A/C]
TATATGCAGTTTCAATTTCATCTTCTGTTTTCTACCACCTCGCAATGTGACAGTTGGTATGAGGAGATCTCATCAAAGTTCACTGATTTTTTATATTGTT

Reverse complement sequence

AACAATATAAAAAATCAGTGAACTTTGATGAGATCTCCTCATACCAACTGTCACATTGCGAGGTGGTAGAAAACAGAAGATGAAATTGAAACTGCATATA[T/G]
CTATACAAAGTGCAACATTAAATTTAATCCAAACCAGACCTGTGATGCCTCCTCTGCCCTATCTGATGCTTCAGCTGTAGCTTGTAGGTGTGGCTGTCGG

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	47.80%	33.40%	2.03%	16.76%	NA
All Indica	2759	20.50%	49.80%	2.86%	26.79%	NA
All Japonica	1512	96.90%	1.20%	0.07%	1.85%	NA
Aus	269	28.30%	62.50%	5.58%	3.72%	NA
Indica I	595	8.10%	71.40%	2.02%	18.49%	NA
Indica II	465	7.30%	54.40%	1.29%	36.99%	NA
Indica III	913	32.20%	32.60%	5.15%	30.01%	NA
Indica Intermediate	786	24.20%	50.80%	1.78%	23.28%	NA
Temperate Japonica	767	98.30%	0.10%	0.13%	1.43%	NA
Tropical Japonica	504	96.20%	1.00%	0.00%	2.78%	NA
Japonica Intermediate	241	93.80%	5.00%	0.00%	1.24%	NA
VI/Aromatic	96	87.50%	7.30%	0.00%	5.21%	NA
Intermediate	90	77.80%	10.00%	1.11%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219745087	A -> C	LOC_Os12g32690.1	upstream_gene_variant ; 1966.0bp to feature; MODIFIER	silent_mutation	Average:14.392; most accessible tissue: Callus, score: 37.925	N	N	N	N
vg1219745087	A -> C	LOC_Os12g32700.1	downstream_gene_variant ; 2737.0bp to feature; MODIFIER	silent_mutation	Average:14.392; most accessible tissue: Callus, score: 37.925	N	N	N	N
vg1219745087	A -> C	LOC_Os12g32690-LOC_Os12g32700	intergenic_region ; MODIFIER	silent_mutation	Average:14.392; most accessible tissue: Callus, score: 37.925	N	N	N	N
vg1219745087	A -> DEL	N	N	silent_mutation	Average:14.392; most accessible tissue: Callus, score: 37.925	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219745087	NA	6.61E-09	mr1575	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
vg1219745087	NA	1.61E-06	mr1832	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
vg1219745087	4.09E-07	8.98E-08	mr1662_2	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
vg1219745087	1.48E-06	3.02E-08	mr1662_2	Ind_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