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Detailed information for vg0820664167:

Variant ID: vg0820664167 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 20664167
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:

AAGGAGAATGAAACAGAAGCTTTTCAAGCACTGTTACCAAGCTTTTGGCAGGTAAAAACATAAGCTTTTATGCTACCAAGCAGGAATATTCGCACAAAAA[G/A]
ATGTCGGGATATCACTCCAACTTCACTTGCAAGTTGGCGCTAGTGGTCCTAGGAATCGTCCGAACGTATGGATACACCCTTAGGGTTCTAAGCTTTTGAA

Reverse complement sequence

TTCAAAAGCTTAGAACCCTAAGGGTGTATCCATACGTTCGGACGATTCCTAGGACCACTAGCGCCAACTTGCAAGTGAAGTTGGAGTGATATCCCGACAT[C/T]
TTTTTGTGCGAATATTCCTGCTTGGTAGCATAAAAGCTTATGTTTTTACCTGCCAAAAGCTTGGTAACAGTGCTTGAAAAGCTTCTGTTTCATTCTCCTT

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	96.00%	3.80%	0.25%	0.00%	NA
All Indica	2759	94.20%	5.80%	0.04%	0.00%	NA
All Japonica	1512	99.30%	0.10%	0.60%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	89.70%	10.30%	0.00%	0.00%	NA
Indica III	913	93.30%	6.70%	0.00%	0.00%	NA
Indica Intermediate	786	93.50%	6.40%	0.13%	0.00%	NA
Temperate Japonica	767	99.00%	0.00%	1.04%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	85.40%	13.50%	1.04%	0.00%	NA
Intermediate	90	93.30%	5.60%	1.11%	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
vg0820664167	G -> A	LOC_Os08g33200.1	downstream_gene_variant ; 1958.0bp to feature; MODIFIER	silent_mutation	Average:57.703; most accessible tissue: Minghui63 flower, score: 73.71	N	N	N	N
vg0820664167	G -> A	LOC_Os08g33190-LOC_Os08g33200	intergenic_region ; MODIFIER	silent_mutation	Average:57.703; most accessible tissue: Minghui63 flower, score: 73.71	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0820664167	NA	2.13E-11	mr1301	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
vg0820664167	NA	2.03E-09	mr1410	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
vg0820664167	NA	6.88E-07	mr1411	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
vg0820664167	NA	2.04E-07	mr1089_2	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
vg0820664167	NA	5.80E-09	mr1093_2	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
vg0820664167	NA	1.12E-06	mr1227_2	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
vg0820664167	NA	3.68E-09	mr1235_2	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
vg0820664167	NA	2.79E-06	mr1243_2	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
vg0820664167	4.63E-06	NA	mr1301_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
vg0820664167	NA	1.81E-06	mr1403_2	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
vg0820664167	7.11E-07	1.44E-17	mr1410_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
vg0820664167	NA	2.14E-06	mr1423_2	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
vg0820664167	1.42E-06	6.55E-08	mr1622_2	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
vg0820664167	NA	1.65E-08	mr1993_2	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