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Detailed information for vg1207208550:

Variant ID: vg1207208550 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7208550
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.15, A: 0.02, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

ATATAAATCACACTTAAAGTACTATGAATGATAAAATAACTCATAACAAAATAAATAATAATTACGTAAATTTTTTGAATAATACGAATGGTCAAACATG[T/C]
GAGAAAAAGTCAACGGCATCATCTATTATAAAACAGAGGGAGTACCTGTTACTACCACACTCACAAATCGCAAATGCGTAAACGTCTCCTAACACACGCT

Reverse complement sequence

AGCGTGTGTTAGGAGACGTTTACGCATTTGCGATTTGTGAGTGTGGTAGTAACAGGTACTCCCTCTGTTTTATAATAGATGATGCCGTTGACTTTTTCTC[A/G]
CATGTTTGACCATTCGTATTATTCAAAAAATTTACGTAATTATTATTTATTTTGTTATGAGTTATTTTATCATTCATAGTACTTTAAGTGTGATTTATAT

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	49.00%	48.60%	1.59%	0.87%	NA
All Indica	2759	78.70%	17.20%	2.61%	1.49%	NA
All Japonica	1512	5.10%	94.80%	0.13%	0.00%	NA
Aus	269	14.50%	85.50%	0.00%	0.00%	NA
Indica I	595	72.40%	14.60%	7.73%	5.21%	NA
Indica II	465	86.70%	13.30%	0.00%	0.00%	NA
Indica III	913	84.60%	14.90%	0.33%	0.22%	NA
Indica Intermediate	786	71.90%	24.20%	2.93%	1.02%	NA
Temperate Japonica	767	5.10%	94.70%	0.26%	0.00%	NA
Tropical Japonica	504	6.30%	93.70%	0.00%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	3.10%	96.90%	0.00%	0.00%	NA
Intermediate	90	26.70%	72.20%	1.11%	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
vg1207208550	T -> C	LOC_Os12g13010.1	upstream_gene_variant ; 1834.0bp to feature; MODIFIER	silent_mutation	Average:49.759; most accessible tissue: Callus, score: 71.635	N	N	N	N
vg1207208550	T -> C	LOC_Os12g13000-LOC_Os12g13010	intergenic_region ; MODIFIER	silent_mutation	Average:49.759; most accessible tissue: Callus, score: 71.635	N	N	N	N
vg1207208550	T -> DEL	N	N	silent_mutation	Average:49.759; most accessible tissue: Callus, score: 71.635	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207208550	NA	3.41E-10	mr1174	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
vg1207208550	NA	2.21E-06	mr1347	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
vg1207208550	NA	5.68E-06	mr1582	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
vg1207208550	NA	4.82E-06	mr1734	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
vg1207208550	NA	7.74E-07	mr1772	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
vg1207208550	NA	3.97E-06	mr1772	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
vg1207208550	NA	1.97E-06	mr1024_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