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Detailed information for vg1211097492:

Variant ID: vg1211097492 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 11097492
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

CAGCTCAGCATCAACAGCAAAGTCAACTAAAGATTTTTCGGACATTCTGAAAACTTCTCAGACAAGTCCGAAAACAACCTTCTGTACGTTTCTGGGAAGT[C/T]
CGAAAAAACACAGAAGTGATTTTGACTCTACTGAGGATTTTCGGAAAAACCGAAAATCAATTTCGGACAAGTCCGAAAATATACAGAACCACTTTTGCCC

Reverse complement sequence

GGGCAAAAGTGGTTCTGTATATTTTCGGACTTGTCCGAAATTGATTTTCGGTTTTTCCGAAAATCCTCAGTAGAGTCAAAATCACTTCTGTGTTTTTTCG[G/A]
ACTTCCCAGAAACGTACAGAAGGTTGTTTTCGGACTTGTCTGAGAAGTTTTCAGAATGTCCGAAAAATCTTTAGTTGACTTTGCTGTTGATGCTGAGCTG

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	64.80%	35.20%	0.02%	0.00%	NA
All Indica	2759	75.30%	24.70%	0.00%	0.00%	NA
All Japonica	1512	59.30%	40.60%	0.07%	0.00%	NA
Aus	269	4.10%	95.90%	0.00%	0.00%	NA
Indica I	595	53.30%	46.70%	0.00%	0.00%	NA
Indica II	465	77.00%	23.00%	0.00%	0.00%	NA
Indica III	913	87.20%	12.80%	0.00%	0.00%	NA
Indica Intermediate	786	77.10%	22.90%	0.00%	0.00%	NA
Temperate Japonica	767	87.40%	12.60%	0.00%	0.00%	NA
Tropical Japonica	504	17.30%	82.50%	0.20%	0.00%	NA
Japonica Intermediate	241	58.10%	41.90%	0.00%	0.00%	NA
VI/Aromatic	96	20.80%	79.20%	0.00%	0.00%	NA
Intermediate	90	63.30%	36.70%	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
vg1211097492	C -> T	LOC_Os12g19120.1	upstream_gene_variant ; 3394.0bp to feature; MODIFIER	silent_mutation	Average:27.656; most accessible tissue: Callus, score: 58.223	N	N	N	N
vg1211097492	C -> T	LOC_Os12g19110-LOC_Os12g19120	intergenic_region ; MODIFIER	silent_mutation	Average:27.656; most accessible tissue: Callus, score: 58.223	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1211097492	NA	1.41E-07	mr1460	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
vg1211097492	NA	4.48E-06	mr1616	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
vg1211097492	NA	6.97E-06	mr1633	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
vg1211097492	NA	9.18E-06	mr1639	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
vg1211097492	NA	8.86E-06	mr1700	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
vg1211097492	NA	1.42E-12	mr1706	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
vg1211097492	NA	2.67E-07	mr1706	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
vg1211097492	NA	4.50E-07	mr1170_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
vg1211097492	NA	7.12E-06	mr1358_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
vg1211097492	NA	4.04E-07	mr1578_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