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Detailed information for vg1115409967:

Variant ID: vg1115409967 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 15409967
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.05, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

TCTAGTATTCAGATAGATGACTTTTGATCAATCTTGTGTTCCCTTAGTTGTGTGTAGGGTTGTTGGTTGTGTGCACTTTCGTGGTGCAGAGGCCGCGAGT[G/A]
TACTAAGACTCTTGAGTTCAATAAAGCTTCCATTATATACAAAACCTAAGGGTGTATGTGGCTAACCCACAAATCCACTTATAAGTTAAATATGGGTTAG

Reverse complement sequence

CTAACCCATATTTAACTTATAAGTGGATTTGTGGGTTAGCCACATACACCCTTAGGTTTTGTATATAATGGAAGCTTTATTGAACTCAAGAGTCTTAGTA[C/T]
ACTCGCGGCCTCTGCACCACGAAAGTGCACACAACCAACAACCCTACACACAACTAAGGGAACACAAGATTGATCAAAAGTCATCTATCTGAATACTAGA

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	63.90%	35.70%	0.25%	0.08%	NA
All Indica	2759	48.40%	51.00%	0.43%	0.14%	NA
All Japonica	1512	98.30%	1.70%	0.00%	0.00%	NA
Aus	269	17.10%	82.90%	0.00%	0.00%	NA
Indica I	595	17.10%	82.50%	0.34%	0.00%	NA
Indica II	465	59.40%	39.80%	0.65%	0.22%	NA
Indica III	913	60.90%	38.70%	0.22%	0.22%	NA
Indica Intermediate	786	51.00%	48.20%	0.64%	0.13%	NA
Temperate Japonica	767	97.90%	2.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.40%	1.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	72.20%	27.80%	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
vg1115409967	G -> A	LOC_Os11g26830.1	upstream_gene_variant ; 697.0bp to feature; MODIFIER	silent_mutation	Average:51.768; most accessible tissue: Callus, score: 78.112	N	N	N	N
vg1115409967	G -> A	LOC_Os11g26830-LOC_Os11g26840	intergenic_region ; MODIFIER	silent_mutation	Average:51.768; most accessible tissue: Callus, score: 78.112	N	N	N	N
vg1115409967	G -> DEL	N	N	silent_mutation	Average:51.768; most accessible tissue: Callus, score: 78.112	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1115409967	NA	4.33E-06	mr1077	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
vg1115409967	6.68E-06	5.19E-15	mr1097	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
vg1115409967	NA	1.08E-06	mr1097	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
vg1115409967	NA	3.80E-06	mr1149	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
vg1115409967	NA	7.37E-06	mr1715	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
vg1115409967	NA	1.58E-08	mr1829	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
vg1115409967	NA	1.21E-09	mr1829	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
vg1115409967	NA	8.58E-07	mr1842	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
vg1115409967	NA	1.27E-13	mr1902	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
vg1115409967	NA	1.37E-07	mr1902	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
vg1115409967	NA	6.16E-07	mr1092_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
vg1115409967	1.22E-06	1.48E-16	mr1097_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
vg1115409967	7.30E-07	2.04E-10	mr1097_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
vg1115409967	NA	4.97E-06	mr1102_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
vg1115409967	NA	4.18E-07	mr1152_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
vg1115409967	8.56E-08	NA	mr1154_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
vg1115409967	2.53E-08	1.00E-13	mr1154_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