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Detailed information for vg0407098060:

Variant ID: vg0407098060 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7098060
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, G: 0.06, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

AACTCTGAAAAGACAGTGAAATGCTTTTCCACTTGCAGATACAGGAAAAATTGGTAAACAAAAATAACAGTCGGCCCTGATTTCTTCCTCTTATCCCTTA[A/G]
TTTAAGAGGCAAGGACTGACATCAAGTTTACAAATTTTCAAAGTGGGTATAAAGTGATACATCTTAAACTCTGCTTAGTATAGCATAACATGAGAAAGCA

Reverse complement sequence

TGCTTTCTCATGTTATGCTATACTAAGCAGAGTTTAAGATGTATCACTTTATACCCACTTTGAAAATTTGTAAACTTGATGTCAGTCCTTGCCTCTTAAA[T/C]
TAAGGGATAAGAGGAAGAAATCAGGGCCGACTGTTATTTTTGTTTACCAATTTTTCCTGTATCTGCAAGTGGAAAAGCATTTCACTGTCTTTTCAGAGTT

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	23.80%	22.50%	0.49%	53.26%	NA
All Indica	2759	2.90%	31.30%	0.69%	65.13%	NA
All Japonica	1512	64.90%	1.20%	0.13%	33.73%	NA
Aus	269	0.40%	43.10%	0.00%	56.51%	NA
Indica I	595	1.50%	20.30%	1.01%	77.14%	NA
Indica II	465	3.20%	41.30%	1.08%	54.41%	NA
Indica III	913	3.20%	31.50%	0.22%	65.06%	NA
Indica Intermediate	786	3.40%	33.30%	0.76%	62.47%	NA
Temperate Japonica	767	97.90%	0.40%	0.00%	1.69%	NA
Tropical Japonica	504	11.50%	1.80%	0.40%	86.31%	NA
Japonica Intermediate	241	71.80%	2.50%	0.00%	25.73%	NA
VI/Aromatic	96	34.40%	40.60%	2.08%	22.92%	NA
Intermediate	90	32.20%	27.80%	0.00%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0407098060	A -> DEL	N	N	silent_mutation	Average:26.122; most accessible tissue: Callus, score: 76.152	N	N	N	N
vg0407098060	A -> G	LOC_Os04g12850.1	downstream_gene_variant ; 2601.0bp to feature; MODIFIER	silent_mutation	Average:26.122; most accessible tissue: Callus, score: 76.152	N	N	N	N
vg0407098060	A -> G	LOC_Os04g12830-LOC_Os04g12850	intergenic_region ; MODIFIER	silent_mutation	Average:26.122; most accessible tissue: Callus, score: 76.152	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0407098060	1.01E-08	1.79E-11	mr1410	Jap_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
vg0407098060	NA	2.36E-06	mr1846	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
vg0407098060	NA	1.47E-10	mr1846_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
vg0407098060	6.99E-06	4.25E-06	mr1855_2	Jap_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