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Detailed information for vg0811517885:

Variant ID: vg0811517885 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 11517885
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, T: 0.26, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCCAACACCATGAACAGAAGCATGTGACCCATTCCCCATTAGGACGGTGGAACCCCGTGCGACCTGATAAGAAGAAAACAATGAGATGTCAACACAAA[C/T]
ATGTACATTGGCCCCTGTATCAACCCACCAATTAGTAGACTGATTAACTGAAAAAATAGTAGGTAAATTACCATACCCGCTTCCATCTCCAGTGTTGCCA

Reverse complement sequence

TGGCAACACTGGAGATGGAAGCGGGTATGGTAATTTACCTACTATTTTTTCAGTTAATCAGTCTACTAATTGGTGGGTTGATACAGGGGCCAATGTACAT[G/A]
TTTGTGTTGACATCTCATTGTTTTCTTCTTATCAGGTCGCACGGGGTTCCACCGTCCTAATGGGGAATGGGTCACATGCTTCTGTTCATGGTGTTGGCAC

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	64.60%	35.10%	0.25%	0.00%	NA
All Indica	2759	89.60%	10.00%	0.33%	0.00%	NA
All Japonica	1512	16.80%	83.10%	0.07%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	97.30%	2.50%	0.17%	0.00%	NA
Indica II	465	91.40%	8.40%	0.22%	0.00%	NA
Indica III	913	83.40%	16.20%	0.44%	0.00%	NA
Indica Intermediate	786	90.10%	9.50%	0.38%	0.00%	NA
Temperate Japonica	767	5.30%	94.70%	0.00%	0.00%	NA
Tropical Japonica	504	33.10%	66.70%	0.20%	0.00%	NA
Japonica Intermediate	241	19.10%	80.90%	0.00%	0.00%	NA
VI/Aromatic	96	12.50%	87.50%	0.00%	0.00%	NA
Intermediate	90	52.20%	45.60%	2.22%	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
vg0811517885	C -> T	LOC_Os08g19260.1	downstream_gene_variant ; 1910.0bp to feature; MODIFIER	silent_mutation	Average:39.619; most accessible tissue: Minghui63 flag leaf, score: 63.692	N	N	N	N
vg0811517885	C -> T	LOC_Os08g19250.1	intron_variant ; MODIFIER	silent_mutation	Average:39.619; most accessible tissue: Minghui63 flag leaf, score: 63.692	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0811517885	NA	8.73E-08	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
vg0811517885	NA	1.72E-06	mr1135	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
vg0811517885	NA	1.31E-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
vg0811517885	NA	3.38E-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
vg0811517885	NA	4.65E-08	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
vg0811517885	NA	5.51E-08	mr1672	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
vg0811517885	NA	1.12E-08	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
vg0811517885	9.16E-07	9.15E-07	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
vg0811517885	NA	2.15E-12	mr1595_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
vg0811517885	NA	1.87E-08	mr1600_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
vg0811517885	NA	1.88E-06	mr1672_2	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
vg0811517885	NA	1.49E-06	mr1841_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
vg0811517885	NA	9.95E-06	mr1900_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