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Detailed information for vg0608469056:

Variant ID: vg0608469056 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8469056
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.68, G: 0.33, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TGTAAGTTCAAAGGAAGATGTAGTTTCAGTCTTGTTGCAGAATCTCCAGAAGGATTTTGCTCTTAAGGATCGTGGAGAGCTGCACTACTTTCTTGGTATA[A/G]
AGGTAACAAAAGCTTCCAATGGAATTTTGTTGACACAATAAAAATATATCTCTGATTTACTGAAAAGAACTGGCATGAGTGATTGTAAATCAGTTAATAC

Reverse complement sequence

GTATTAACTGATTTACAATCACTCATGCCAGTTCTTTTCAGTAAATCAGAGATATATTTTTATTGTGTCAACAAAATTCCATTGGAAGCTTTTGTTACCT[T/C]
TATACCAAGAAAGTAGTGCAGCTCTCCACGATCCTTAAGAGCAAAATCCTTCTGGAGATTCTGCAACAAGACTGAAACTACATCTTCCTTTGAACTTACA

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	42.70%	31.80%	0.25%	25.29%	NA
All Indica	2759	5.30%	52.70%	0.43%	41.57%	NA
All Japonica	1512	99.00%	0.90%	0.00%	0.13%	NA
Aus	269	86.20%	0.70%	0.00%	13.01%	NA
Indica I	595	5.40%	45.70%	0.84%	48.07%	NA
Indica II	465	4.90%	79.10%	0.22%	15.70%	NA
Indica III	913	4.50%	37.30%	0.33%	57.83%	NA
Indica Intermediate	786	6.40%	60.20%	0.38%	33.08%	NA
Temperate Japonica	767	99.00%	0.90%	0.00%	0.13%	NA
Tropical Japonica	504	99.20%	0.60%	0.00%	0.20%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	52.20%	37.80%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0608469056	A -> G	LOC_Os06g14920.1	missense_variant&splice_region_variant ; p.Lys257Glu; MODERATE	nonsynonymous_codon ; K257E	Average:26.13; most accessible tissue: Callus, score: 83.628	benign	-0.917	TOLERATED	1.00
vg0608469056	A -> DEL	LOC_Os06g14920.1	N	frameshift_variant	Average:26.13; most accessible tissue: Callus, score: 83.628	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608469056	9.78E-06	5.59E-16	mr1228	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