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Detailed information for vg1118813179:

Variant ID: vg1118813179 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18813179
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.11, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

GCCATATATACATTAATACATGCCCTAATTCCGCACGCAGTTCGTCGCCCTAGCTAACTCCTAGGCACGCATGCATGCCCTAATTTAATCACTTCCATCA[C/T]
CTCACATCAAGAAGGGAGCAGCAATCATATGCACAATACTGTATTTAATTGTTTTTATACTTGTAATCATGGACCATGCATGGTGCATGGATCGATGGAC

Reverse complement sequence

GTCCATCGATCCATGCACCATGCATGGTCCATGATTACAAGTATAAAAACAATTAAATACAGTATTGTGCATATGATTGCTGCTCCCTTCTTGATGTGAG[G/A]
TGATGGAAGTGATTAAATTAGGGCATGCATGCGTGCCTAGGAGTTAGCTAGGGCGACGAACTGCGTGCGGAATTAGGGCATGTATTAATGTATATATGGC

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	85.00%	10.80%	0.23%	3.94%	NA
All Indica	2759	82.90%	10.20%	0.40%	6.56%	NA
All Japonica	1512	98.40%	1.60%	0.00%	0.00%	NA
Aus	269	28.30%	71.70%	0.00%	0.00%	NA
Indica I	595	94.60%	4.20%	0.17%	1.01%	NA
Indica II	465	91.60%	2.60%	0.43%	5.38%	NA
Indica III	913	70.40%	18.50%	0.44%	10.62%	NA
Indica Intermediate	786	83.20%	9.50%	0.51%	6.74%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	96.00%	4.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	5.20%	0.00%	5.21%	NA
Intermediate	90	92.20%	7.80%	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
vg1118813179	C -> T	LOC_Os11g31970-LOC_Os11g31980	intergenic_region ; MODIFIER	silent_mutation	Average:37.697; most accessible tissue: Callus, score: 92.5	N	N	N	N
vg1118813179	C -> DEL	N	N	silent_mutation	Average:37.697; most accessible tissue: Callus, score: 92.5	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118813179	NA	6.29E-15	mr1113	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
vg1118813179	NA	1.17E-20	mr1817	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
vg1118813179	4.26E-07	NA	mr1118_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
vg1118813179	7.75E-06	NA	mr1123_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
vg1118813179	NA	1.63E-19	mr1240_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
vg1118813179	2.83E-06	NA	mr1496_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
vg1118813179	NA	6.21E-19	mr1817_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