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Detailed information for vg1109628487:

Variant ID: vg1109628487 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9628487
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TCCGATACACATTAAATGTTTTTTCTGTTAGTGCACGGTGCCTGATTTTATGTTTTCTTAGTAAGATGGTTACTCAGTTTACAGTTACATGTCTTTGTCC[C/A]
TGCAGTAACACAAACCTTACTTTGCAGTAACATATTTTATTTTTTGCAGTAACTCATCTATGTGCTTTATCCTTTTTTCATGCAGTGGGTTCAGTTGTTA

Reverse complement sequence

TAACAACTGAACCCACTGCATGAAAAAAGGATAAAGCACATAGATGAGTTACTGCAAAAAATAAAATATGTTACTGCAAAGTAAGGTTTGTGTTACTGCA[G/T]
GGACAAAGACATGTAACTGTAAACTGAGTAACCATCTTACTAAGAAAACATAAAATCAGGCACCGTGCACTAACAGAAAAAACATTTAATGTGTATCGGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.50%	0.50%	4.38%	57.60%	NA
All Indica	2759	9.30%	0.90%	6.60%	83.18%	NA
All Japonica	1512	95.60%	0.00%	0.07%	4.37%	NA
Aus	269	4.80%	0.00%	5.95%	89.22%	NA
Indica I	595	15.30%	2.50%	7.39%	74.79%	NA
Indica II	465	3.40%	0.60%	1.29%	94.62%	NA
Indica III	913	6.00%	0.00%	9.64%	84.34%	NA
Indica Intermediate	786	12.10%	0.90%	5.60%	81.42%	NA
Temperate Japonica	767	96.90%	0.00%	0.00%	3.13%	NA
Tropical Japonica	504	93.50%	0.00%	0.00%	6.55%	NA
Japonica Intermediate	241	95.90%	0.00%	0.41%	3.73%	NA
VI/Aromatic	96	20.80%	0.00%	3.12%	76.04%	NA
Intermediate	90	41.10%	0.00%	5.56%	53.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109628487	C -> A	LOC_Os11g17280.1	upstream_gene_variant ; 1958.0bp to feature; MODIFIER	silent_mutation	Average:27.339; most accessible tissue: Callus, score: 72.187	N	N	N	N
vg1109628487	C -> A	LOC_Os11g17290.1	intron_variant ; MODIFIER	silent_mutation	Average:27.339; most accessible tissue: Callus, score: 72.187	N	N	N	N
vg1109628487	C -> A	LOC_Os11g17290.2	intron_variant ; MODIFIER	silent_mutation	Average:27.339; most accessible tissue: Callus, score: 72.187	N	N	N	N
vg1109628487	C -> A	LOC_Os11g17290.3	intron_variant ; MODIFIER	silent_mutation	Average:27.339; most accessible tissue: Callus, score: 72.187	N	N	N	N
vg1109628487	C -> DEL	N	N	silent_mutation	Average:27.339; most accessible tissue: Callus, score: 72.187	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109628487	NA	7.89E-06	mr1019_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
vg1109628487	NA	7.72E-07	mr1275_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
vg1109628487	1.88E-06	1.88E-06	mr1344_2	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
vg1109628487	NA	7.08E-06	mr1405_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
vg1109628487	NA	1.90E-06	mr1608_2	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
vg1109628487	NA	4.59E-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
vg1109628487	4.78E-06	4.78E-06	mr1704_2	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
vg1109628487	NA	3.34E-11	mr1781_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
vg1109628487	1.60E-06	1.59E-06	mr1783_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
vg1109628487	7.29E-06	2.03E-06	mr1789_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
vg1109628487	2.47E-06	2.47E-06	mr1804_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
vg1109628487	3.55E-06	3.97E-06	mr1827_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