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Detailed information for vg1117624908:

Variant ID: vg1117624908 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17624908
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: 254. )

Flanking Sequence (100 bp) in Reference Genome:

CTCTTAACTTTAATTTTTTTAAAAAAACTAGATGAACTAGAATAATTTACTTAAAAACTCTAGTACAAACGACTGACAATCTGAAATAGCTGACACAGAT[G/A]
TAGTCAACTTCTTTTAGTGGTCACACACAAGACTCATCACATAAATGATGAATTATGAAGAGTTCATATAACTCGATCGAGAGGGGAACAACTAAAGTGA

Reverse complement sequence

TCACTTTAGTTGTTCCCCTCTCGATCGAGTTATATGAACTCTTCATAATTCATCATTTATGTGATGAGTCTTGTGTGTGACCACTAAAAGAAGTTGACTA[C/T]
ATCTGTGTCAGCTATTTCAGATTGTCAGTCGTTTGTACTAGAGTTTTTAAGTAAATTATTCTAGTTCATCTAGTTTTTTTAAAAAAATTAAAGTTAAGAG

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	82.40%	17.40%	0.21%	0.00%	NA
All Indica	2759	71.40%	28.30%	0.36%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	53.90%	45.40%	0.67%	0.00%	NA
Indica II	465	65.60%	34.40%	0.00%	0.00%	NA
Indica III	913	84.60%	15.30%	0.11%	0.00%	NA
Indica Intermediate	786	72.60%	26.70%	0.64%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	84.40%	15.60%	0.00%	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
vg1117624908	G -> A	LOC_Os11g30360.1	upstream_gene_variant ; 880.0bp to feature; MODIFIER	silent_mutation	Average:46.087; most accessible tissue: Zhenshan97 flower, score: 67.623	N	N	N	N
vg1117624908	G -> A	LOC_Os11g30350-LOC_Os11g30360	intergenic_region ; MODIFIER	silent_mutation	Average:46.087; most accessible tissue: Zhenshan97 flower, score: 67.623	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117624908	6.72E-07	1.93E-07	mr1800	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
vg1117624908	6.44E-08	2.65E-10	mr1800	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