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Detailed information for vg1121560983:

Variant ID: vg1121560983 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21560983
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACCAGTATAAATGATCTAATGGTTTAGATTAATTTGATCTTCCACTCAATTAGCTTGTAATATAAATTGACAAAGGGTATATTTGTCTTTCAACTAGGT[G/A]
AAACCCCGCGCATTGCTGCGGGAATTTAGTATGATAACAATAAAAAAAATAACGTGCAAGATAGCTAGATAACATCAGATTAAGTAAATTAATGTGGTTT

Reverse complement sequence

AAACCACATTAATTTACTTAATCTGATGTTATCTAGCTATCTTGCACGTTATTTTTTTTATTGTTATCATACTAAATTCCCGCAGCAATGCGCGGGGTTT[C/T]
ACCTAGTTGAAAGACAAATATACCCTTTGTCAATTTATATTACAAGCTAATTGAGTGGAAGATCAAATTAATCTAAACCATTAGATCATTTATACTGGTA

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	63.10%	2.10%	0.61%	34.21%	NA
All Indica	2759	54.10%	1.60%	0.83%	43.49%	NA
All Japonica	1512	81.70%	0.70%	0.20%	17.39%	NA
Aus	269	62.50%	16.40%	1.12%	20.07%	NA
Indica I	595	64.90%	5.20%	0.67%	29.24%	NA
Indica II	465	46.90%	0.00%	1.29%	51.83%	NA
Indica III	913	49.90%	0.70%	0.77%	48.63%	NA
Indica Intermediate	786	55.00%	0.90%	0.76%	43.38%	NA
Temperate Japonica	767	90.40%	1.20%	0.26%	8.21%	NA
Tropical Japonica	504	71.80%	0.20%	0.20%	27.78%	NA
Japonica Intermediate	241	74.70%	0.40%	0.00%	24.90%	NA
VI/Aromatic	96	21.90%	0.00%	0.00%	78.12%	NA
Intermediate	90	71.10%	1.10%	0.00%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121560983	G -> A	LOC_Os11g36530.1	upstream_gene_variant ; 4556.0bp to feature; MODIFIER	silent_mutation	Average:22.746; most accessible tissue: Callus, score: 56.849	N	N	N	N
vg1121560983	G -> A	LOC_Os11g36550.1	upstream_gene_variant ; 857.0bp to feature; MODIFIER	silent_mutation	Average:22.746; most accessible tissue: Callus, score: 56.849	N	N	N	N
vg1121560983	G -> A	LOC_Os11g36530-LOC_Os11g36550	intergenic_region ; MODIFIER	silent_mutation	Average:22.746; most accessible tissue: Callus, score: 56.849	N	N	N	N
vg1121560983	G -> DEL	N	N	silent_mutation	Average:22.746; most accessible tissue: Callus, score: 56.849	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121560983	1.53E-06	9.38E-06	mr1011	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