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Detailed information for vg0811646982:

Variant ID: vg0811646982 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 11646982
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

GCAGCATTTAGCAAATATTTGAGAATTATAAAACAGTAGAATAATTAATCATTAATATTAATCAACACTGAACAGCACACCCATGCTGCTCAGGCCCAAC[C/T]
ATCCTGAACAACCATACCCGGCTGCACAGATTTATCTCCAAACCAGGAATGTACCATTCTGACGGAGCGTGGGACTCCTCACCGGGAGACCGCGCAGGCC

Reverse complement sequence

GGCCTGCGCGGTCTCCCGGTGAGGAGTCCCACGCTCCGTCAGAATGGTACATTCCTGGTTTGGAGATAAATCTGTGCAGCCGGGTATGGTTGTTCAGGAT[G/A]
GTTGGGCCTGAGCAGCATGGGTGTGCTGTTCAGTGTTGATTAATATTAATGATTAATTATTCTACTGTTTTATAATTCTCAAATATTTGCTAAATGCTGC

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	50.90%	48.60%	0.42%	0.00%	NA
All Indica	2759	83.10%	16.50%	0.43%	0.00%	NA
All Japonica	1512	2.00%	97.80%	0.20%	0.00%	NA
Aus	269	19.00%	81.00%	0.00%	0.00%	NA
Indica I	595	96.60%	3.20%	0.17%	0.00%	NA
Indica II	465	85.80%	13.50%	0.65%	0.00%	NA
Indica III	913	76.50%	23.20%	0.33%	0.00%	NA
Indica Intermediate	786	79.00%	20.40%	0.64%	0.00%	NA
Temperate Japonica	767	2.10%	97.90%	0.00%	0.00%	NA
Tropical Japonica	504	1.20%	98.60%	0.20%	0.00%	NA
Japonica Intermediate	241	3.30%	95.90%	0.83%	0.00%	NA
VI/Aromatic	96	3.10%	94.80%	2.08%	0.00%	NA
Intermediate	90	33.30%	63.30%	3.33%	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
vg0811646982	C -> T	LOC_Os08g19490.1	upstream_gene_variant ; 2363.0bp to feature; MODIFIER	silent_mutation	Average:33.628; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0811646982	C -> T	LOC_Os08g19500.1	upstream_gene_variant ; 1881.0bp to feature; MODIFIER	silent_mutation	Average:33.628; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0811646982	C -> T	LOC_Os08g19480.1	downstream_gene_variant ; 4448.0bp to feature; MODIFIER	silent_mutation	Average:33.628; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0811646982	C -> T	LOC_Os08g19490-LOC_Os08g19500	intergenic_region ; MODIFIER	silent_mutation	Average:33.628; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0811646982	NA	1.59E-08	mr1457	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
vg0811646982	NA	8.06E-17	mr1484	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
vg0811646982	3.99E-06	6.50E-07	mr1484	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
vg0811646982	NA	3.46E-11	mr1609	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
vg0811646982	NA	5.37E-23	mr1841	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
vg0811646982	NA	7.08E-10	mr1945	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