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Detailed information for vg1108517495:

Variant ID: vg1108517495 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8517495
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GTCGGAATCGGCTCAATCGGCTAACCTTGTCCGACTCAAACTCTGCCGATTATGATCGTAGCCGATTCGGACTTAGCCGATTCTTGCTCTGTTTCCGAAA[C/T]
GATCTTGATCTTGGATTCCGCTTCGATCCTATCTTCATCTCCGACACTTGGATTACCAAATTTGGTTGTTAACATCGGTAGAGCGTCAGCAATACATCCT

Reverse complement sequence

AGGATGTATTGCTGACGCTCTACCGATGTTAACAACCAAATTTGGTAATCCAAGTGTCGGAGATGAAGATAGGATCGAAGCGGAATCCAAGATCAAGATC[G/A]
TTTCGGAAACAGAGCAAGAATCGGCTAAGTCCGAATCGGCTACGATCATAATCGGCAGAGTTTGAGTCGGACAAGGTTAGCCGATTGAGCCGATTCCGAC

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	91.90%	8.10%	0.02%	0.00%	NA
All Indica	2759	89.50%	10.50%	0.00%	0.00%	NA
All Japonica	1512	98.90%	1.10%	0.00%	0.00%	NA
Aus	269	74.70%	24.90%	0.37%	0.00%	NA
Indica I	595	89.60%	10.40%	0.00%	0.00%	NA
Indica II	465	96.30%	3.70%	0.00%	0.00%	NA
Indica III	913	87.10%	12.90%	0.00%	0.00%	NA
Indica Intermediate	786	88.20%	11.80%	0.00%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	97.40%	2.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg1108517495	C -> T	LOC_Os11g15120.1	upstream_gene_variant ; 1803.0bp to feature; MODIFIER	silent_mutation	Average:30.701; most accessible tissue: Zhenshan97 young leaf, score: 55.261	N	N	N	N
vg1108517495	C -> T	LOC_Os11g15120-LOC_Os11g15130	intergenic_region ; MODIFIER	silent_mutation	Average:30.701; most accessible tissue: Zhenshan97 young leaf, score: 55.261	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108517495	NA	5.87E-06	mr1043	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
vg1108517495	7.34E-06	8.87E-10	mr1705	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