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Detailed information for vg0813660047:

Variant ID: vg0813660047 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 13660047
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.66, C: 0.34, others allele: 0.00, population size: 50. )

Flanking Sequence (100 bp) in Reference Genome:

CATAGCTCGAGGATTGTATTTACAAAATAGCTTTGAGCAACTAAATGTCCTTAATGCTGTTTACTGCAAACCCTAACCCCTTATATTAAAACCCCCATTG[T/C]
ACTCCCTTGCATTTATTCTACACTTGTGGGTGTGTCTTGTTGAGTACGGTGGTTGTACTCAGTCTTGCTCAATTTTTCCCAAACCCAGAAGTGGAGTTCC

Reverse complement sequence

GGAACTCCACTTCTGGGTTTGGGAAAAATTGAGCAAGACTGAGTACAACCACCGTACTCAACAAGACACACCCACAAGTGTAGAATAAATGCAAGGGAGT[A/G]
CAATGGGGGTTTTAATATAAGGGGTTAGGGTTTGCAGTAAACAGCATTAAGGACATTTAGTTGCTCAAAGCTATTTTGTAAATACAATCCTCGAGCTATG

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	36.60%	3.60%	3.91%	55.86%	NA
All Indica	2759	16.00%	5.80%	5.22%	72.96%	NA
All Japonica	1512	66.70%	0.30%	1.79%	31.28%	NA
Aus	269	84.00%	1.90%	0.74%	13.38%	NA
Indica I	595	6.60%	3.20%	5.04%	85.21%	NA
Indica II	465	12.50%	5.20%	5.16%	77.20%	NA
Indica III	913	21.50%	8.80%	5.37%	64.40%	NA
Indica Intermediate	786	19.00%	4.70%	5.22%	71.12%	NA
Temperate Japonica	767	93.20%	0.10%	0.26%	6.39%	NA
Tropical Japonica	504	38.50%	0.20%	2.98%	58.33%	NA
Japonica Intermediate	241	41.10%	0.80%	4.15%	53.94%	NA
VI/Aromatic	96	19.80%	0.00%	6.25%	73.96%	NA
Intermediate	90	41.10%	0.00%	6.67%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0813660047	T -> C	LOC_Os08g22710.1	downstream_gene_variant ; 3220.0bp to feature; MODIFIER	silent_mutation	Average:23.558; most accessible tissue: Zhenshan97 root, score: 34.536	N	N	N	N
vg0813660047	T -> C	LOC_Os08g22710-LOC_Os08g22740	intergenic_region ; MODIFIER	silent_mutation	Average:23.558; most accessible tissue: Zhenshan97 root, score: 34.536	N	N	N	N
vg0813660047	T -> DEL	N	N	silent_mutation	Average:23.558; most accessible tissue: Zhenshan97 root, score: 34.536	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0813660047	NA	3.35E-06	mr1069	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
vg0813660047	NA	9.12E-06	mr1134	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
vg0813660047	NA	1.95E-07	mr1238	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
vg0813660047	NA	2.85E-06	mr1309	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
vg0813660047	NA	3.25E-08	mr1321	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
vg0813660047	NA	2.97E-09	mr1342	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
vg0813660047	NA	2.67E-06	mr1504	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
vg0813660047	NA	7.21E-07	mr1568	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
vg0813660047	NA	3.27E-06	mr1672	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
vg0813660047	4.01E-06	NA	mr1743	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
vg0813660047	NA	9.69E-06	mr1821	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
vg0813660047	NA	1.05E-06	mr1841	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
vg0813660047	NA	1.51E-14	mr1883	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
vg0813660047	1.31E-06	1.30E-06	mr1883	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
vg0813660047	2.16E-06	2.16E-06	mr1900	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
vg0813660047	NA	9.91E-12	mr1914	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
vg0813660047	NA	2.88E-08	mr1672_2	Jap_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