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Detailed information for vg1209068690:

Variant ID: vg1209068690 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9068690
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.74, C: 0.26, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

CATTGAGTTTCAATTAAATTTTATTTAAATCTCTACAATCCGCACTATGGTAAAACAAGAAAATACAATCCAAACACAAGGCACACACACGTTAGACTAC[T/C]
GGTAGTGAGACTATAAGATGATGACAATAACTGTTCTCGCGTTGAAGAAACACTGCACATTTATACTACATCGGTCGACAAATATAAGAATCTTAGTACA

Reverse complement sequence

TGTACTAAGATTCTTATATTTGTCGACCGATGTAGTATAAATGTGCAGTGTTTCTTCAACGCGAGAACAGTTATTGTCATCATCTTATAGTCTCACTACC[A/G]
GTAGTCTAACGTGTGTGTGCCTTGTGTTTGGATTGTATTTTCTTGTTTTACCATAGTGCGGATTGTAGAGATTTAAATAAAATTTAATTGAAACTCAATG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.40%	43.50%	0.08%	0.00%	NA
All Indica	2759	82.70%	17.10%	0.14%	0.00%	NA
All Japonica	1512	2.40%	97.60%	0.00%	0.00%	NA
Aus	269	90.00%	10.00%	0.00%	0.00%	NA
Indica I	595	81.20%	18.70%	0.17%	0.00%	NA
Indica II	465	78.10%	21.90%	0.00%	0.00%	NA
Indica III	913	88.10%	11.90%	0.00%	0.00%	NA
Indica Intermediate	786	80.40%	19.20%	0.38%	0.00%	NA
Temperate Japonica	767	1.60%	98.40%	0.00%	0.00%	NA
Tropical Japonica	504	3.40%	96.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.90%	97.10%	0.00%	0.00%	NA
VI/Aromatic	96	76.00%	24.00%	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
vg1209068690	T -> C	LOC_Os12g15920.1	upstream_gene_variant ; 328.0bp to feature; MODIFIER	silent_mutation	Average:44.214; most accessible tissue: Callus, score: 76.323	N	N	N	N
vg1209068690	T -> C	LOC_Os12g15910-LOC_Os12g15920	intergenic_region ; MODIFIER	silent_mutation	Average:44.214; most accessible tissue: Callus, score: 76.323	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209068690	NA	7.21E-06	mr1047_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
vg1209068690	NA	5.47E-13	mr1722_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
vg1209068690	1.04E-06	1.50E-07	mr1722_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