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Detailed information for vg1116820455:

Variant ID: vg1116820455 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16820455
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

CATGTCATACACACATGTGCTCTTCTCTCCTATTTTATATCCTTAAAATATGTTTATAGCTGGCTTGTAGTCCACTATTGTAGCTGCTCTAATGCGCGGC[G/A]
CGCTCGCCCCACCTGCCTCGCTCCTGGCTCGCGGCTGGATATCTTCTATCTCTCAATCGTTCTAGATGTACCGTAAGTAACATATATACAAAAGTATAAG

Reverse complement sequence

CTTATACTTTTGTATATATGTTACTTACGGTACATCTAGAACGATTGAGAGATAGAAGATATCCAGCCGCGAGCCAGGAGCGAGGCAGGTGGGGCGAGCG[C/T]
GCCGCGCATTAGAGCAGCTACAATAGTGGACTACAAGCCAGCTATAAACATATTTTAAGGATATAAAATAGGAGAGAAGAGCACATGTGTGTATGACATG

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	37.70%	29.40%	0.13%	32.73%	NA
All Indica	2759	7.80%	48.60%	0.14%	43.39%	NA
All Japonica	1512	92.60%	1.20%	0.07%	6.15%	NA
Aus	269	13.80%	0.40%	0.00%	85.87%	NA
Indica I	595	12.90%	66.70%	0.00%	20.34%	NA
Indica II	465	1.30%	48.40%	0.43%	49.89%	NA
Indica III	913	7.00%	37.70%	0.00%	55.31%	NA
Indica Intermediate	786	8.80%	47.80%	0.25%	43.13%	NA
Temperate Japonica	767	96.60%	1.30%	0.13%	1.96%	NA
Tropical Japonica	504	88.50%	1.20%	0.00%	10.32%	NA
Japonica Intermediate	241	88.40%	0.80%	0.00%	10.79%	NA
VI/Aromatic	96	93.80%	2.10%	1.04%	3.12%	NA
Intermediate	90	44.40%	30.00%	0.00%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116820455	G -> A	LOC_Os11g29050.1	upstream_gene_variant ; 1124.0bp to feature; MODIFIER	silent_mutation	Average:41.418; most accessible tissue: Zhenshan97 flag leaf, score: 73.119	N	N	N	N
vg1116820455	G -> A	LOC_Os11g29030-LOC_Os11g29050	intergenic_region ; MODIFIER	silent_mutation	Average:41.418; most accessible tissue: Zhenshan97 flag leaf, score: 73.119	N	N	N	N
vg1116820455	G -> DEL	N	N	silent_mutation	Average:41.418; most accessible tissue: Zhenshan97 flag leaf, score: 73.119	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116820455	NA	3.10E-06	mr1346_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1116820455	NA	7.59E-06	mr1346_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1116820455	3.10E-06	3.10E-06	mr1456_2	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