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Detailed information for vg1116560090:

Variant ID: vg1116560090 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16560090
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: 116. )

Flanking Sequence (100 bp) in Reference Genome:

ATATATGCCGGCGTCTCTTCTACTACTCCTCGGTATTTATGCATGACGCCGTTAACTTTTTAACAAATATTTAACCTTTCATTTTATTCAAAAAATTTAT[G/A]
TAATTATCATTTATTTTATTGTGATTTGATTTATCATCAAATGTTCTTTAAGCATGACATAAGTATTTTTGTATTTGCATAAAAAAATTAAATAAGTCGA

Reverse complement sequence

TCGACTTATTTAATTTTTTTATGCAAATACAAAAATACTTATGTCATGCTTAAAGAACATTTGATGATAAATCAAATCACAATAAAATAAATGATAATTA[C/T]
ATAAATTTTTTGAATAAAATGAAAGGTTAAATATTTGTTAAAAAGTTAACGGCGTCATGCATAAATACCGAGGAGTAGTAGAAGAGACGCCGGCATATAT

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	81.10%	12.80%	4.74%	1.35%	NA
All Indica	2759	75.80%	19.90%	2.68%	1.59%	NA
All Japonica	1512	95.70%	3.20%	0.20%	0.86%	NA
Aus	269	44.20%	0.00%	53.16%	2.60%	NA
Indica I	595	88.60%	10.30%	1.01%	0.17%	NA
Indica II	465	88.40%	7.30%	1.72%	2.58%	NA
Indica III	913	59.40%	35.50%	3.40%	1.75%	NA
Indica Intermediate	786	77.70%	16.70%	3.69%	1.91%	NA
Temperate Japonica	767	98.60%	0.90%	0.26%	0.26%	NA
Tropical Japonica	504	90.70%	7.50%	0.00%	1.79%	NA
Japonica Intermediate	241	97.10%	1.70%	0.41%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	88.90%	7.80%	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
vg1116560090	G -> A	LOC_Os11g28640.1	upstream_gene_variant ; 1622.0bp to feature; MODIFIER	silent_mutation	Average:35.549; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1116560090	G -> A	LOC_Os11g28640-LOC_Os11g28650	intergenic_region ; MODIFIER	silent_mutation	Average:35.549; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1116560090	G -> DEL	N	N	silent_mutation	Average:35.549; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116560090	1.60E-06	1.60E-06	mr1584	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