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Detailed information for vg0810479074:

Variant ID: vg0810479074 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 10479074
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTTTATTGATAAGTTCTTAAAGGGAATATGCAGCTCACATGGTGTCCGCTGAGTGATGTCATCAACGGGGCAGGTGGTTTCGTCCTGGGTTTGCATGGC[G/A]
TCCATGCTTTGTGATCCTACCTGCCCTGTTGAGGCGCAGCTGCTACGATTTCCTGAAGGGCTCATCATTGCAGGAGGAATGGTCGGCTGGGGATCATGGG

Reverse complement sequence

CCCATGATCCCCAGCCGACCATTCCTCCTGCAATGATGAGCCCTTCAGGAAATCGTAGCAGCTGCGCCTCAACAGGGCAGGTAGGATCACAAAGCATGGA[C/T]
GCCATGCAAACCCAGGACGAAACCACCTGCCCCGTTGATGACATCACTCAGCGGACACCATGTGAGCTGCATATTCCCTTTAAGAACTTATCAATAAAGG

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	88.40%	10.70%	0.93%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	70.50%	27.60%	1.85%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	97.70%	2.20%	0.13%	0.00%	NA
Tropical Japonica	504	39.30%	57.50%	3.17%	0.00%	NA
Japonica Intermediate	241	49.40%	46.10%	4.56%	0.00%	NA
VI/Aromatic	96	18.80%	67.70%	13.54%	0.00%	NA
Intermediate	90	75.60%	21.10%	3.33%	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
vg0810479074	G -> A	LOC_Os08g17130.1	downstream_gene_variant ; 3955.0bp to feature; MODIFIER	silent_mutation	Average:31.511; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N
vg0810479074	G -> A	LOC_Os08g17120.1	intron_variant ; MODIFIER	silent_mutation	Average:31.511; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0810479074	NA	7.61E-12	mr1454	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
vg0810479074	8.68E-06	NA	mr1083_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
vg0810479074	4.03E-07	NA	mr1103_2	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
vg0810479074	NA	5.27E-09	mr1379_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
vg0810479074	NA	1.29E-06	mr1559_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