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Detailed information for vg0409860484:

Variant ID: vg0409860484 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 9860484
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.54, G: 0.46, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

TGACCGGAATGAAAAAGTTCAAAAAGCACCAAAACTTGATTCTTGGAGAAACTGGAGTGTATTGGGTGTGTTCGTGGCAAAAAATCACTTCGTGATTCGC[G/A]
CGGTGAACTTTTGTCAATTAACGCCAATATTGGCACACGTGGGTGCGATGTTTTCGACCGGAACAAAAAAGTTCAAAAAGCACCAAAACATGATTTTCGG

Reverse complement sequence

CCGAAAATCATGTTTTGGTGCTTTTTGAACTTTTTTGTTCCGGTCGAAAACATCGCACCCACGTGTGCCAATATTGGCGTTAATTGACAAAAGTTCACCG[C/T]
GCGAATCACGAAGTGATTTTTTGCCACGAACACACCCAATACACTCCAGTTTCTCCAAGAATCAAGTTTTGGTGCTTTTTGAACTTTTTCATTCCGGTCA

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	60.20%	23.00%	1.71%	15.09%	NA
All Indica	2759	95.50%	0.90%	0.14%	3.48%	NA
All Japonica	1512	1.70%	67.50%	3.70%	27.18%	NA
Aus	269	49.10%	1.90%	1.49%	47.58%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	96.30%	2.40%	0.00%	1.29%	NA
Indica III	913	92.60%	0.40%	0.22%	6.79%	NA
Indica Intermediate	786	95.30%	0.90%	0.25%	3.56%	NA
Temperate Japonica	767	0.40%	96.50%	0.26%	2.87%	NA
Tropical Japonica	504	2.40%	20.20%	8.93%	68.45%	NA
Japonica Intermediate	241	4.10%	73.90%	3.73%	18.26%	NA
VI/Aromatic	96	8.30%	14.60%	13.54%	63.54%	NA
Intermediate	90	51.10%	25.60%	4.44%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0409860484	G -> DEL	N	N	silent_mutation	Average:31.351; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N
vg0409860484	G -> A	LOC_Os04g17930.1	upstream_gene_variant ; 3269.0bp to feature; MODIFIER	silent_mutation	Average:31.351; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N
vg0409860484	G -> A	LOC_Os04g17940.1	downstream_gene_variant ; 1916.0bp to feature; MODIFIER	silent_mutation	Average:31.351; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N
vg0409860484	G -> A	LOC_Os04g17930-LOC_Os04g17940	intergenic_region ; MODIFIER	silent_mutation	Average:31.351; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0409860484	NA	3.72E-14	mr1010	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
vg0409860484	9.98E-08	NA	mr1392	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
vg0409860484	NA	1.31E-40	mr1890	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
vg0409860484	NA	3.08E-39	mr1891	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
vg0409860484	NA	2.71E-20	mr1010_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