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Detailed information for vg0808721437:

Variant ID: vg0808721437 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8721437
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAACTAATTTCATAACTCGTCTGTAAACCGCGAGATGAATTTATTAAGAGAAAATTCCCTATATACCCCTGAAAATTTACTCAATCCCTTCAATACCCCT[G/A]
AATTTGACATCATCCCTTATATACCCCTGAGTTTTCATTTTGATCTCCTCTATACCCATCTCCGTTAGTTGACCATTAGTTGACCGTTAAATATTTTAAA

Reverse complement sequence

TTTAAAATATTTAACGGTCAACTAATGGTCAACTAACGGAGATGGGTATAGAGGAGATCAAAATGAAAACTCAGGGGTATATAAGGGATGATGTCAAATT[C/T]
AGGGGTATTGAAGGGATTGAGTAAATTTTCAGGGGTATATAGGGAATTTTCTCTTAATAAATTCATCTCGCGGTTTACAGACGAGTTATGAAATTAGTTT

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	83.50%	11.70%	2.14%	2.67%	NA
All Indica	2759	72.30%	19.70%	3.52%	4.49%	NA
All Japonica	1512	99.80%	0.10%	0.00%	0.07%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	76.50%	19.50%	2.69%	1.34%	NA
Indica II	465	82.60%	6.90%	2.58%	7.96%	NA
Indica III	913	61.20%	27.30%	5.26%	6.24%	NA
Indica Intermediate	786	76.00%	18.60%	2.67%	2.80%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.00%	0.20%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	90.00%	6.70%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0808721437	G -> A	LOC_Os08g14510.1	upstream_gene_variant ; 3527.0bp to feature; MODIFIER	silent_mutation	Average:32.279; most accessible tissue: Minghui63 root, score: 52.955	N	N	N	N
vg0808721437	G -> A	LOC_Os08g14520.1	upstream_gene_variant ; 4322.0bp to feature; MODIFIER	silent_mutation	Average:32.279; most accessible tissue: Minghui63 root, score: 52.955	N	N	N	N
vg0808721437	G -> A	LOC_Os08g14500-LOC_Os08g14510	intergenic_region ; MODIFIER	silent_mutation	Average:32.279; most accessible tissue: Minghui63 root, score: 52.955	N	N	N	N
vg0808721437	G -> DEL	N	N	silent_mutation	Average:32.279; most accessible tissue: Minghui63 root, score: 52.955	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808721437	1.11E-06	3.24E-07	mr1333	Ind_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