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Detailed information for vg1116817015:

Variant ID: vg1116817015 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16817015
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

CCGATATTGCTCTTATTCACCATAATCACACCAGTACAATATGTGAGGTAACCTATCTAACTATTGTCGACATGGCGGTCTGAAGGTCTGACTCGTAGTC[G/A]
ACAATAGGGTAGTCTTCCTCCTCGAATATGTACCCAGCGAGATCAGAGATAATGCTTTCGTCTCTCCTGATAGTATCCGGAGACACCATAGGAGACTAGC

Reverse complement sequence

GCTAGTCTCCTATGGTGTCTCCGGATACTATCAGGAGAGACGAAAGCATTATCTCTGATCTCGCTGGGTACATATTCGAGGAGGAAGACTACCCTATTGT[C/T]
GACTACGAGTCAGACCTTCAGACCGCCATGTCGACAATAGTTAGATAGGTTACCTCACATATTGTACTGGTGTGATTATGGTGAATAAGAGCAATATCGG

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	35.80%	32.20%	2.22%	29.81%	NA
All Indica	2759	3.60%	53.20%	3.48%	39.69%	NA
All Japonica	1512	93.00%	1.20%	0.53%	5.29%	NA
Aus	269	21.60%	0.40%	0.37%	77.70%	NA
Indica I	595	2.40%	77.50%	0.17%	20.00%	NA
Indica II	465	2.20%	48.80%	7.74%	41.29%	NA
Indica III	913	2.40%	41.80%	3.18%	52.57%	NA
Indica Intermediate	786	6.70%	50.80%	3.82%	38.68%	NA
Temperate Japonica	767	96.70%	1.30%	0.00%	1.96%	NA
Tropical Japonica	504	88.70%	1.20%	0.20%	9.92%	NA
Japonica Intermediate	241	90.00%	0.80%	2.90%	6.22%	NA
VI/Aromatic	96	94.80%	2.10%	0.00%	3.12%	NA
Intermediate	90	40.00%	35.60%	0.00%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116817015	G -> A	LOC_Os11g29050.1	upstream_gene_variant ; 4564.0bp to feature; MODIFIER	silent_mutation	Average:31.137; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg1116817015	G -> A	LOC_Os11g29030-LOC_Os11g29050	intergenic_region ; MODIFIER	silent_mutation	Average:31.137; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg1116817015	G -> DEL	N	N	silent_mutation	Average:31.137; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116817015	NA	1.75E-08	mr1342	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
vg1116817015	4.64E-06	4.64E-06	mr1572	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