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Detailed information for vg1208774850:

Variant ID: vg1208774850 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8774850
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.05, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

GCCCCTCATCGGCGAACACAGGAAGGAAATTTTCCTCAAAAACTTTTCGTTAACACGAGAGCAAGTTTTTTACTTTGCAGGAACACAACATAGGTTTCGG[T/C]
AGGAGCATCAGCCGAAAGGGGGCGCCTCGTGGTATACCATACGACTTACACGGTCTCGGCCGAAGCTCCCTACTCACCCTTGCCCGTGAGAGGCTTGTTG

Reverse complement sequence

CAACAAGCCTCTCACGGGCAAGGGTGAGTAGGGAGCTTCGGCCGAGACCGTGTAAGTCGTATGGTATACCACGAGGCGCCCCCTTTCGGCTGATGCTCCT[A/G]
CCGAAACCTATGTTGTGTTCCTGCAAAGTAAAAAACTTGCTCTCGTGTTAACGAAAAGTTTTTGAGGAAAATTTCCTTCCTGTGTTCGCCGATGAGGGGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.10%	20.40%	9.23%	34.24%	NA
All Indica	2759	6.70%	33.00%	14.24%	46.10%	NA
All Japonica	1512	94.80%	0.60%	0.33%	4.23%	NA
Aus	269	4.10%	3.30%	2.97%	89.59%	NA
Indica I	595	4.70%	23.00%	5.88%	66.39%	NA
Indica II	465	12.50%	24.90%	13.76%	48.82%	NA
Indica III	913	3.40%	44.70%	19.50%	32.42%	NA
Indica Intermediate	786	8.50%	31.70%	14.76%	45.04%	NA
Temperate Japonica	767	93.50%	0.80%	0.39%	5.35%	NA
Tropical Japonica	504	95.80%	0.60%	0.40%	3.17%	NA
Japonica Intermediate	241	97.10%	0.00%	0.00%	2.90%	NA
VI/Aromatic	96	27.10%	29.20%	19.79%	23.96%	NA
Intermediate	90	56.70%	11.10%	12.22%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208774850	T -> C	LOC_Os12g15370.1	intron_variant ; MODIFIER	silent_mutation	Average:20.943; most accessible tissue: Callus, score: 53.325	N	N	N	N
vg1208774850	T -> DEL	N	N	silent_mutation	Average:20.943; most accessible tissue: Callus, score: 53.325	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208774850	NA	8.15E-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
vg1208774850	NA	9.51E-07	mr1186_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
vg1208774850	NA	5.72E-06	mr1186_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
vg1208774850	NA	6.91E-06	mr1245_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
vg1208774850	NA	4.51E-06	mr1268_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
vg1208774850	NA	2.92E-06	mr1268_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
vg1208774850	NA	3.52E-06	mr1373_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
vg1208774850	NA	1.35E-06	mr1477_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
vg1208774850	NA	2.23E-06	mr1648_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
vg1208774850	NA	6.09E-06	mr1648_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
vg1208774850	7.06E-06	7.05E-06	mr1651_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
vg1208774850	NA	5.31E-07	mr1655_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
vg1208774850	NA	9.06E-07	mr1669_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
vg1208774850	NA	2.57E-06	mr1682_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
vg1208774850	NA	9.39E-06	mr1683_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
vg1208774850	1.78E-06	1.79E-06	mr1697_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
vg1208774850	4.42E-06	4.42E-06	mr1697_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
vg1208774850	NA	8.22E-06	mr1756_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
vg1208774850	NA	1.04E-06	mr1851_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
vg1208774850	NA	8.10E-07	mr1971_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