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Detailed information for vg0818948966:

Variant ID: vg0818948966 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18948966
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTATGTTCTTTCCACGACACCCTACCCATTCTCTTGTAAAGGAATTCGTAGATACAGGGCCGTGTAAACAGAGTAGCTATGTATATATTCTTATTAGCGA[G/A]
AGGAGGAAAGTGTGTGAGACCTCTATTTCTGGTGCTTAATTCTGGTCCTTTGCCCTGCAGGTGTAAACTATCTCTATATATGCATGATGACAAAGACAAA

Reverse complement sequence

TTTGTCTTTGTCATCATGCATATATAGAGATAGTTTACACCTGCAGGGCAAAGGACCAGAATTAAGCACCAGAAATAGAGGTCTCACACACTTTCCTCCT[C/T]
TCGCTAATAAGAATATATACATAGCTACTCTGTTTACACGGCCCTGTATCTACGAATTCCTTTACAAGAGAATGGGTAGGGTGTCGTGGAAAGAACATAC

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	93.80%	6.20%	0.00%	0.00%	NA
All Indica	2759	89.60%	10.40%	0.00%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	95.30%	4.70%	0.00%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	81.40%	18.60%	0.00%	0.00%	NA
Indica Intermediate	786	89.40%	10.60%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0818948966	G -> A	LOC_Os08g30719.1	downstream_gene_variant ; 1398.0bp to feature; MODIFIER	silent_mutation	Average:55.347; most accessible tissue: Zhenshan97 young leaf, score: 69.263	N	N	N	N
vg0818948966	G -> A	LOC_Os08g30710-LOC_Os08g30719	intergenic_region ; MODIFIER	silent_mutation	Average:55.347; most accessible tissue: Zhenshan97 young leaf, score: 69.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818948966	NA	3.13E-06	mr1131	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
vg0818948966	7.80E-07	3.94E-08	mr1768	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
vg0818948966	NA	1.80E-07	mr1798	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