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Detailed information for vg0223792839:

Variant ID: vg0223792839 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23792839
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.10, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

CCACTTCTCATGCCAATCGGGGCTAACACATTGGCACTCTCCGCTGCTTTAATGATCCGGTGAAAAGGCTCCATAGCTAAAATAAACAGCATCGGGGACA[G/A]
GGGATCTCCCTGACGGAGTCCCCTAGCATGATTAATTCTCATCCCTAGGGAACCATTTAGGAGCACTTGGGACGAGGAGGTGGAAAACAGATTAGAGATC

Reverse complement sequence

GATCTCTAATCTGTTTTCCACCTCCTCGTCCCAAGTGCTCCTAAATGGTTCCCTAGGGATGAGAATTAATCATGCTAGGGGACTCCGTCAGGGAGATCCC[C/T]
TGTCCCCGATGCTGTTTATTTTAGCTATGGAGCCTTTTCACCGGATCATTAAAGCAGCGGAGAGTGCCAATGTGTTAGCCCCGATTGGCATGAGAAGTGG

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	76.50%	12.90%	1.93%	8.74%	NA
All Indica	2759	66.60%	21.00%	1.20%	11.20%	NA
All Japonica	1512	97.50%	0.90%	0.99%	0.60%	NA
Aus	269	61.30%	0.00%	13.01%	25.65%	NA
Indica I	595	66.60%	33.30%	0.00%	0.17%	NA
Indica II	465	45.40%	20.90%	3.01%	30.75%	NA
Indica III	913	73.70%	19.90%	0.99%	5.37%	NA
Indica Intermediate	786	71.00%	13.00%	1.27%	14.76%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	95.00%	0.80%	2.78%	1.39%	NA
Japonica Intermediate	241	96.30%	2.50%	0.41%	0.83%	NA
VI/Aromatic	96	62.50%	6.20%	8.33%	22.92%	NA
Intermediate	90	85.60%	10.00%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0223792839	G -> A	LOC_Os02g39430.1	upstream_gene_variant ; 2702.0bp to feature; MODIFIER	silent_mutation	Average:27.033; most accessible tissue: Zhenshan97 flower, score: 36.732	N	N	N	N
vg0223792839	G -> A	LOC_Os02g39440.1	upstream_gene_variant ; 27.0bp to feature; MODIFIER	silent_mutation	Average:27.033; most accessible tissue: Zhenshan97 flower, score: 36.732	N	N	N	N
vg0223792839	G -> A	LOC_Os02g39450.1	upstream_gene_variant ; 2830.0bp to feature; MODIFIER	silent_mutation	Average:27.033; most accessible tissue: Zhenshan97 flower, score: 36.732	N	N	N	N
vg0223792839	G -> A	LOC_Os02g39440-LOC_Os02g39450	intergenic_region ; MODIFIER	silent_mutation	Average:27.033; most accessible tissue: Zhenshan97 flower, score: 36.732	N	N	N	N
vg0223792839	G -> DEL	N	N	silent_mutation	Average:27.033; most accessible tissue: Zhenshan97 flower, score: 36.732	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223792839	6.47E-06	NA	mr1183_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
vg0223792839	NA	4.00E-06	mr1795_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
vg0223792839	4.38E-06	NA	mr1918_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
vg0223792839	6.33E-06	NA	mr1918_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