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Detailed information for vg1223790057:

Variant ID: vg1223790057 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23790057
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.54, A: 0.46, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

GAACATAAGAGTGGAGGATTTAAAAAAGTAATAATTTAATAGAGAAGGGGTCATAATTAATTCCCTACATGCATGCATGTCTTATATTATGGAGCATTAA[G/A]
AAAATGGTTGTGTCTTATATTATGGAATGGAGGGAGTACCTGCTTACTTCACTCATCAATCAAGTTAAAATAGCGTCAACCGTTTATTTTTCTTTGAGAT

Reverse complement sequence

ATCTCAAAGAAAAATAAACGGTTGACGCTATTTTAACTTGATTGATGAGTGAAGTAAGCAGGTACTCCCTCCATTCCATAATATAAGACACAACCATTTT[C/T]
TTAATGCTCCATAATATAAGACATGCATGCATGTAGGGAATTAATTATGACCCCTTCTCTATTAAATTATTACTTTTTTAAATCCTCCACTCTTATGTTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.20%	28.30%	0.04%	0.40%	NA
All Indica	2759	97.10%	2.30%	0.04%	0.62%	NA
All Japonica	1512	24.10%	75.70%	0.07%	0.13%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	92.90%	4.30%	0.22%	2.58%	NA
Indica III	913	97.70%	2.20%	0.00%	0.11%	NA
Indica Intermediate	786	97.20%	2.30%	0.00%	0.51%	NA
Temperate Japonica	767	15.50%	84.20%	0.00%	0.26%	NA
Tropical Japonica	504	28.40%	71.60%	0.00%	0.00%	NA
Japonica Intermediate	241	42.70%	56.80%	0.41%	0.00%	NA
VI/Aromatic	96	12.50%	87.50%	0.00%	0.00%	NA
Intermediate	90	53.30%	46.70%	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
vg1223790057	G -> DEL	N	N	silent_mutation	Average:60.853; most accessible tissue: Callus, score: 74.468	N	N	N	N
vg1223790057	G -> A	LOC_Os12g38730.1	downstream_gene_variant ; 4280.0bp to feature; MODIFIER	silent_mutation	Average:60.853; most accessible tissue: Callus, score: 74.468	N	N	N	N
vg1223790057	G -> A	LOC_Os12g38730.2	downstream_gene_variant ; 4280.0bp to feature; MODIFIER	silent_mutation	Average:60.853; most accessible tissue: Callus, score: 74.468	N	N	N	N
vg1223790057	G -> A	LOC_Os12g38720-LOC_Os12g38730	intergenic_region ; MODIFIER	silent_mutation	Average:60.853; most accessible tissue: Callus, score: 74.468	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223790057	NA	1.26E-16	mr1118	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
vg1223790057	NA	3.35E-18	mr1242	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
vg1223790057	NA	4.90E-07	mr1680	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
vg1223790057	NA	2.52E-06	mr1681	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
vg1223790057	NA	9.39E-07	mr1881	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
vg1223790057	NA	1.90E-07	mr1321_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
vg1223790057	NA	7.44E-09	mr1645_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
vg1223790057	NA	2.15E-06	mr1648_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
vg1223790057	NA	6.20E-21	mr1657_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
vg1223790057	1.42E-06	1.38E-15	mr1722_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