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Detailed information for vg1111620364:

Variant ID: vg1111620364 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11620364
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCCCATTCATCGGCCATAAGGTTATAATACTCATCGGTTGTTAAAGTATTTTGCAGCTCCGTTCTTCTTGAGCCGATTCTAACCTCCCATGGCAAAAC[G/A]
GCCTCATGACCATAAACAAGTTTATAAGGAGGAACCTGTATCGATCCATGAAAAGCCATCCGATAAGACCATAATGCTTCAGCTAACCGAGTGTGCCATT

Reverse complement sequence

AATGGCACACTCGGTTAGCTGAAGCATTATGGTCTTATCGGATGGCTTTTCATGGATCGATACAGGTTCCTCCTTATAAACTTGTTTATGGTCATGAGGC[C/T]
GTTTTGCCATGGGAGGTTAGAATCGGCTCAAGAAGAACGGAGCTGCAAAATACTTTAACAACCGATGAGTATTATAACCTTATGGCCGATGAATGGGAAG

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	42.80%	37.40%	17.75%	2.03%	NA
All Indica	2759	63.00%	11.30%	25.37%	0.40%	NA
All Japonica	1512	3.40%	87.40%	4.03%	5.22%	NA
Aus	269	74.70%	7.80%	17.47%	0.00%	NA
Indica I	595	55.60%	8.90%	35.46%	0.00%	NA
Indica II	465	72.90%	3.40%	22.15%	1.51%	NA
Indica III	913	64.80%	14.60%	20.26%	0.33%	NA
Indica Intermediate	786	60.40%	13.90%	25.57%	0.13%	NA
Temperate Japonica	767	1.40%	95.30%	1.96%	1.30%	NA
Tropical Japonica	504	6.90%	74.00%	7.14%	11.90%	NA
Japonica Intermediate	241	2.10%	90.00%	4.15%	3.73%	NA
VI/Aromatic	96	3.10%	82.30%	13.54%	1.04%	NA
Intermediate	90	36.70%	37.80%	20.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1111620364	G -> A	LOC_Os11g20110.1	downstream_gene_variant ; 795.0bp to feature; MODIFIER	silent_mutation	Average:7.261; most accessible tissue: Zhenshan97 flag leaf, score: 15.873	N	N	N	N
vg1111620364	G -> A	LOC_Os11g20110-LOC_Os11g20130	intergenic_region ; MODIFIER	silent_mutation	Average:7.261; most accessible tissue: Zhenshan97 flag leaf, score: 15.873	N	N	N	N
vg1111620364	G -> DEL	N	N	silent_mutation	Average:7.261; most accessible tissue: Zhenshan97 flag leaf, score: 15.873	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111620364	2.85E-07	2.85E-07	mr1848	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