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Detailed information for vg1122886718:

Variant ID: vg1122886718 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22886718
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, A: 0.16, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCTAATAAGCCAAAACTTTTTATTAGGAAATAAAATTTATAATTTATAAGTAAAAATTTTATATACATGTTTTAGCAACTTAAAAACTAGGGTAATTT[A/G]
GAACCATGCCATTATAATTTTGCAAAGTTTGAGATATGCCATCGGTATCTCAATGACATGCAAGATCTACATGAGTCAATGACATGTGGGTTAGGATGGC

Reverse complement sequence

GCCATCCTAACCCACATGTCATTGACTCATGTAGATCTTGCATGTCATTGAGATACCGATGGCATATCTCAAACTTTGCAAAATTATAATGGCATGGTTC[T/C]
AAATTACCCTAGTTTTTAAGTTGCTAAAACATGTATATAAAATTTTTACTTATAAATTATAAATTTTATTTCCTAATAAAAAGTTTTGGCTTATTAGGGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.40%	15.00%	3.36%	24.21%	NA
All Indica	2759	68.60%	5.00%	1.59%	24.76%	NA
All Japonica	1512	35.60%	28.10%	6.55%	29.76%	NA
Aus	269	50.20%	46.10%	3.72%	0.00%	NA
Indica I	595	29.40%	5.20%	2.02%	63.36%	NA
Indica II	465	94.20%	2.80%	0.86%	2.15%	NA
Indica III	913	78.30%	6.10%	1.42%	14.13%	NA
Indica Intermediate	786	72.00%	4.80%	1.91%	21.25%	NA
Temperate Japonica	767	21.90%	37.30%	4.43%	36.38%	NA
Tropical Japonica	504	41.30%	17.50%	11.90%	29.37%	NA
Japonica Intermediate	241	67.20%	21.20%	2.07%	9.54%	NA
VI/Aromatic	96	87.50%	6.20%	0.00%	6.25%	NA
Intermediate	90	71.10%	16.70%	6.67%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122886718	A -> DEL	N	N	silent_mutation	Average:42.323; most accessible tissue: Callus, score: 87.349	N	N	N	N
vg1122886718	A -> G	LOC_Os11g38620.1	upstream_gene_variant ; 684.0bp to feature; MODIFIER	silent_mutation	Average:42.323; most accessible tissue: Callus, score: 87.349	N	N	N	N
vg1122886718	A -> G	LOC_Os11g38620.2	upstream_gene_variant ; 684.0bp to feature; MODIFIER	silent_mutation	Average:42.323; most accessible tissue: Callus, score: 87.349	N	N	N	N
vg1122886718	A -> G	LOC_Os11g38610.2	downstream_gene_variant ; 2171.0bp to feature; MODIFIER	silent_mutation	Average:42.323; most accessible tissue: Callus, score: 87.349	N	N	N	N
vg1122886718	A -> G	LOC_Os11g38610-LOC_Os11g38620	intergenic_region ; MODIFIER	silent_mutation	Average:42.323; most accessible tissue: Callus, score: 87.349	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122886718	NA	2.20E-06	mr1236_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
vg1122886718	4.89E-06	2.68E-06	mr1462_2	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
vg1122886718	NA	2.77E-06	mr1704_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
vg1122886718	5.70E-06	5.70E-06	mr1867_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