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Detailed information for vg0321862928:

Variant ID: vg0321862928 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21862928
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

ATATTTACCACTCTATGAAACTTCCAGCGGCTTGATTGTCTAGATATTGTTCTTCTCTTCATACTTAATGCTGCATCAGTTGAGTTTGATTTATTAAGTC[G/A]
TGCTTAGAAGATCAATCTCTAACCTGTCTTCTGGTTGCCGATTAGGGTAGCATCGGAGTTTCAGCCGATCTTATCTGATTTAACTATATTTGCTTTATAT

Reverse complement sequence

ATATAAAGCAAATATAGTTAAATCAGATAAGATCGGCTGAAACTCCGATGCTACCCTAATCGGCAACCAGAAGACAGGTTAGAGATTGATCTTCTAAGCA[C/T]
GACTTAATAAATCAAACTCAACTGATGCAGCATTAAGTATGAAGAGAAGAACAATATCTAGACAATCAAGCCGCTGGAAGTTTCATAGAGTGGTAAATAT

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	69.60%	0.70%	15.51%	14.24%	NA
All Indica	2759	56.40%	1.10%	19.75%	22.80%	NA
All Japonica	1512	98.50%	0.00%	0.46%	1.06%	NA
Aus	269	30.10%	0.00%	63.20%	6.69%	NA
Indica I	595	89.70%	0.00%	2.86%	7.39%	NA
Indica II	465	42.40%	0.90%	12.90%	43.87%	NA
Indica III	913	44.00%	1.50%	35.27%	19.17%	NA
Indica Intermediate	786	53.80%	1.40%	18.58%	26.21%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	95.60%	0.00%	1.39%	2.98%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	74.40%	3.30%	12.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0321862928	G -> A	LOC_Os03g39350.1	upstream_gene_variant ; 3754.0bp to feature; MODIFIER	silent_mutation	Average:33.709; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N
vg0321862928	G -> A	LOC_Os03g39330-LOC_Os03g39350	intergenic_region ; MODIFIER	silent_mutation	Average:33.709; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N
vg0321862928	G -> DEL	N	N	silent_mutation	Average:33.709; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321862928	NA	1.49E-06	mr1517	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
vg0321862928	NA	4.64E-06	mr1689	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
vg0321862928	4.66E-06	3.69E-07	mr1517_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