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Detailed information for vg0820115562:

Variant ID: vg0820115562 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 20115562
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.24, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

TATAAACATTACGTCTTAAAGTCCGTGCTGCAGCTGGCTACAGATCTGTAGCCCGCTGCTCTTCTCTCACTTCCTTTATCTTTTTAAAATATATTTATAG[T/C]
TGGTTTATAGCTTGCTATTGTGCTTGCTCTTAGTTTGAGAAAATCTCATATGTATTTCTGAAATTTTATTTAATCTCATCTATGCGTTTGAGTTTTAGTT

Reverse complement sequence

AACTAAAACTCAAACGCATAGATGAGATTAAATAAAATTTCAGAAATACATATGAGATTTTCTCAAACTAAGAGCAAGCACAATAGCAAGCTATAAACCA[A/G]
CTATAAATATATTTTAAAAAGATAAAGGAAGTGAGAGAAGAGCAGCGGGCTACAGATCTGTAGCCAGCTGCAGCACGGACTTTAAGACGTAATGTTTATA

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	66.50%	33.40%	0.04%	0.00%	NA
All Indica	2759	94.70%	5.30%	0.04%	0.00%	NA
All Japonica	1512	9.90%	90.10%	0.00%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	98.00%	2.00%	0.00%	0.00%	NA
Indica II	465	93.50%	6.50%	0.00%	0.00%	NA
Indica III	913	94.90%	5.00%	0.11%	0.00%	NA
Indica Intermediate	786	92.60%	7.40%	0.00%	0.00%	NA
Temperate Japonica	767	0.90%	99.10%	0.00%	0.00%	NA
Tropical Japonica	504	24.00%	76.00%	0.00%	0.00%	NA
Japonica Intermediate	241	9.10%	90.90%	0.00%	0.00%	NA
VI/Aromatic	96	65.60%	34.40%	0.00%	0.00%	NA
Intermediate	90	60.00%	38.90%	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
vg0820115562	T -> C	LOC_Os08g32480-LOC_Os08g32490	intergenic_region ; MODIFIER	silent_mutation	Average:46.912; most accessible tissue: Callus, score: 96.56	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0820115562	NA	4.45E-10	Grain_weight	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0820115562	NA	2.28E-06	mr1028	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
vg0820115562	NA	2.01E-14	mr1146	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
vg0820115562	NA	2.25E-07	mr1190	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
vg0820115562	NA	4.68E-07	mr1245	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
vg0820115562	NA	2.06E-29	mr1256	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
vg0820115562	NA	8.17E-09	mr1275	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
vg0820115562	NA	5.74E-16	mr1276	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
vg0820115562	NA	5.71E-06	mr1445	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
vg0820115562	6.06E-06	6.43E-07	mr1446	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
vg0820115562	NA	5.53E-07	mr1453	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
vg0820115562	NA	6.77E-06	mr1516	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
vg0820115562	NA	1.52E-17	mr1529	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
vg0820115562	NA	8.40E-11	mr1921	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
vg0820115562	1.27E-06	NA	mr1855_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