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Detailed information for vg0314840946:

Variant ID: vg0314840946 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14840946
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGATTCGTCTCGCAAATTAGCTGCAATCTGCGCAATTAGTTATTTTTTAGCCTATATTTAATACTTCATGTAGGTGTTCAAACGTTCGATGTGACAGG[G/A]
TATAAAATTTTTGTGTGGGAACTTAGGCCATCAGCAACGCGTGCCCCTAGAGAGTAGCCTCGCAAATGACATCCAACTTCCGTCGTCGGGTCGTCCCCTA

Reverse complement sequence

TAGGGGACGACCCGACGACGGAAGTTGGATGTCATTTGCGAGGCTACTCTCTAGGGGCACGCGTTGCTGATGGCCTAAGTTCCCACACAAAAATTTTATA[C/T]
CCTGTCACATCGAACGTTTGAACACCTACATGAAGTATTAAATATAGGCTAAAAAATAACTAATTGCGCAGATTGCAGCTAATTTGCGAGACGAATCTTT

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	87.50%	9.90%	2.29%	0.25%	NA
All Indica	2759	79.20%	16.50%	3.84%	0.43%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	78.00%	14.30%	7.39%	0.34%	NA
Indica II	465	83.70%	13.10%	3.23%	0.00%	NA
Indica III	913	80.10%	18.40%	1.10%	0.44%	NA
Indica Intermediate	786	76.50%	18.10%	4.71%	0.76%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	90.00%	7.80%	2.22%	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
vg0314840946	G -> A	LOC_Os03g25920.1	upstream_gene_variant ; 1824.0bp to feature; MODIFIER	silent_mutation	Average:76.1; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0314840946	G -> A	LOC_Os03g25930.1	downstream_gene_variant ; 2875.0bp to feature; MODIFIER	silent_mutation	Average:76.1; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0314840946	G -> A	LOC_Os03g25920-LOC_Os03g25930	intergenic_region ; MODIFIER	silent_mutation	Average:76.1; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0314840946	G -> DEL	N	N	silent_mutation	Average:76.1; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314840946	7.97E-09	NA	mr1542	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
vg0314840946	4.88E-07	2.67E-11	mr1542	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
vg0314840946	3.10E-07	NA	mr1542_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
vg0314840946	2.62E-06	5.41E-11	mr1542_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