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Detailed information for vg0804860838:

Variant ID: vg0804860838 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4860838
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: 39. )

Flanking Sequence (100 bp) in Reference Genome:

AAACATGTCGAATTTTCACAAGAAAATTAAAGAGAAGATCGGATCTTGATTACTGCTAAATGGAATAGTTGGTCTTTTTTTTATTTCACATGCATGATCT[G/A]
AATGGGATAGTTCTAGTATGGTCTCAGATCTTGTCAACGTAATCAGATGTGCCGTAGTATTGTTTTGAGCGCGACAGGGCCGAGCGTGATCACCACAGGG

Reverse complement sequence

CCCTGTGGTGATCACGCTCGGCCCTGTCGCGCTCAAAACAATACTACGGCACATCTGATTACGTTGACAAGATCTGAGACCATACTAGAACTATCCCATT[C/T]
AGATCATGCATGTGAAATAAAAAAAAGACCAACTATTCCATTTAGCAGTAATCAAGATCCGATCTTCTCTTTAATTTTCTTGTGAAAATTCGACATGTTT

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	47.50%	11.80%	17.37%	23.32%	NA
All Indica	2759	35.20%	12.60%	25.55%	26.68%	NA
All Japonica	1512	80.80%	0.10%	2.25%	16.87%	NA
Aus	269	1.90%	72.50%	15.24%	10.41%	NA
Indica I	595	22.90%	1.70%	34.79%	40.67%	NA
Indica II	465	43.20%	6.70%	18.49%	31.61%	NA
Indica III	913	40.10%	24.80%	22.12%	13.03%	NA
Indica Intermediate	786	34.10%	10.20%	26.72%	29.01%	NA
Temperate Japonica	767	89.60%	0.00%	2.61%	7.82%	NA
Tropical Japonica	504	73.80%	0.20%	0.99%	25.00%	NA
Japonica Intermediate	241	67.60%	0.00%	3.73%	28.63%	NA
VI/Aromatic	96	9.40%	10.40%	21.88%	58.33%	NA
Intermediate	90	42.20%	5.60%	22.22%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0804860838	G -> A	LOC_Os08g08440.1	upstream_gene_variant ; 1734.0bp to feature; MODIFIER	silent_mutation	Average:34.494; most accessible tissue: Minghui63 flag leaf, score: 67.635	N	N	N	N
vg0804860838	G -> A	LOC_Os08g08440-LOC_Os08g08450	intergenic_region ; MODIFIER	silent_mutation	Average:34.494; most accessible tissue: Minghui63 flag leaf, score: 67.635	N	N	N	N
vg0804860838	G -> DEL	N	N	silent_mutation	Average:34.494; most accessible tissue: Minghui63 flag leaf, score: 67.635	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804860838	7.26E-06	NA	mr1800_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