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Detailed information for vg0805645286:

Variant ID: vg0805645286 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5645286
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.65, A: 0.34, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

ACGAATCTATTGAGTCTAATTAATCCATGATTAGCCTATGTGATGCTATAGTAAACATTATCTAATTATGAATTAATTAGGCTTAAAAAATTTGTCTCAC[G/A]
AATTAGCTTTCATTTATGTAATTAGTTTTGTAAGTAGTCTATATTTAATACTCTAAATTAGTGTCTAAATATAGAGACTAAAGTTAAGTCTCTGGATCCA

Reverse complement sequence

TGGATCCAGAGACTTAACTTTAGTCTCTATATTTAGACACTAATTTAGAGTATTAAATATAGACTACTTACAAAACTAATTACATAAATGAAAGCTAATT[C/T]
GTGAGACAAATTTTTTAAGCCTAATTAATTCATAATTAGATAATGTTTACTATAGCATCACATAGGCTAATCATGGATTAATTAGACTCAATAGATTCGT

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	51.90%	47.60%	0.38%	0.08%	NA
All Indica	2759	38.60%	60.90%	0.43%	0.14%	NA
All Japonica	1512	88.20%	11.70%	0.07%	0.00%	NA
Aus	269	0.40%	98.90%	0.74%	0.00%	NA
Indica I	595	44.20%	55.00%	0.34%	0.50%	NA
Indica II	465	77.00%	21.90%	0.86%	0.22%	NA
Indica III	913	14.20%	85.40%	0.33%	0.00%	NA
Indica Intermediate	786	39.80%	59.80%	0.38%	0.00%	NA
Temperate Japonica	767	98.20%	1.70%	0.13%	0.00%	NA
Tropical Japonica	504	76.20%	23.80%	0.00%	0.00%	NA
Japonica Intermediate	241	81.70%	18.30%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	58.90%	37.80%	3.33%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0805645286	G -> A	LOC_Os08g09760.1	downstream_gene_variant ; 2012.0bp to feature; MODIFIER	silent_mutation	Average:36.113; most accessible tissue: Callus, score: 69.292	N	N	N	N
vg0805645286	G -> A	LOC_Os08g09770.1	downstream_gene_variant ; 391.0bp to feature; MODIFIER	silent_mutation	Average:36.113; most accessible tissue: Callus, score: 69.292	N	N	N	N
vg0805645286	G -> A	LOC_Os08g09760.2	downstream_gene_variant ; 2021.0bp to feature; MODIFIER	silent_mutation	Average:36.113; most accessible tissue: Callus, score: 69.292	N	N	N	N
vg0805645286	G -> A	LOC_Os08g09760-LOC_Os08g09770	intergenic_region ; MODIFIER	silent_mutation	Average:36.113; most accessible tissue: Callus, score: 69.292	N	N	N	N
vg0805645286	G -> DEL	N	N	silent_mutation	Average:36.113; most accessible tissue: Callus, score: 69.292	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805645286	NA	2.32E-07	mr1851_2	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
vg0805645286	7.40E-06	6.44E-10	mr1864_2	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
vg0805645286	1.72E-06	1.72E-06	mr1982_2	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