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Detailed information for vg0820873126:

Variant ID: vg0820873126 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 20873126
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.66, A: 0.34, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

GATCTATGAATATTACCTGAAATCGGCGTCTGAATCCGGTAGGGCTTCGCCCCTTCTTCTCTTCTCCTCCCCTTTCTTCTTTTTTTTCACTGGATTTGAG[A/G]
GGGGAGGAATGAGGGCTGGGAGCTGGGCGGCAGGCCTTTTATAGGCAGCGAGGCCTGCCGCCCGGCCAGAGGGCGGCAAGGGGCCGCCTGCAAAATGCCG

Reverse complement sequence

CGGCATTTTGCAGGCGGCCCCTTGCCGCCCTCTGGCCGGGCGGCAGGCCTCGCTGCCTATAAAAGGCCTGCCGCCCAGCTCCCAGCCCTCATTCCTCCCC[T/C]
CTCAAATCCAGTGAAAAAAAAGAAGAAAGGGGAGGAGAAGAGAAGAAGGGGCGAAGCCCTACCGGATTCAGACGCCGATTTCAGGTAATATTCATAGATC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.60%	1.40%	10.98%	48.96%	NA
All Indica	2759	4.90%	2.10%	12.29%	80.75%	NA
All Japonica	1512	98.70%	0.10%	0.13%	1.12%	NA
Aus	269	19.70%	2.60%	62.45%	15.24%	NA
Indica I	595	3.00%	1.20%	3.87%	91.93%	NA
Indica II	465	1.70%	3.00%	7.31%	87.96%	NA
Indica III	913	6.20%	2.40%	19.17%	72.18%	NA
Indica Intermediate	786	6.50%	1.90%	13.61%	77.99%	NA
Temperate Japonica	767	99.10%	0.00%	0.00%	0.91%	NA
Tropical Japonica	504	97.80%	0.20%	0.20%	1.79%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	96.90%	0.00%	1.04%	2.08%	NA
Intermediate	90	60.00%	1.10%	10.00%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0820873126	A -> G	LOC_Os08g33450.1	upstream_gene_variant ; 855.0bp to feature; MODIFIER	silent_mutation	Average:25.34; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0820873126	A -> G	LOC_Os08g33460.1	upstream_gene_variant ; 426.0bp to feature; MODIFIER	silent_mutation	Average:25.34; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0820873126	A -> G	LOC_Os08g33450-LOC_Os08g33460	intergenic_region ; MODIFIER	silent_mutation	Average:25.34; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0820873126	A -> DEL	N	N	silent_mutation	Average:25.34; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0820873126	NA	6.09E-08	mr1610	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
vg0820873126	NA	3.21E-15	mr1916	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
vg0820873126	NA	2.84E-13	mr1151_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
vg0820873126	NA	7.47E-09	mr1198_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
vg0820873126	NA	3.76E-07	mr1205_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
vg0820873126	NA	3.87E-10	mr1228_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
vg0820873126	NA	1.26E-07	mr1302_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
vg0820873126	NA	2.86E-07	mr1376_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
vg0820873126	7.67E-06	7.67E-06	mr1412_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
vg0820873126	NA	3.18E-08	mr1418_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
vg0820873126	1.88E-06	1.88E-06	mr1418_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
vg0820873126	NA	7.04E-06	mr1419_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
vg0820873126	1.31E-06	1.31E-06	mr1419_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
vg0820873126	NA	9.71E-06	mr1420_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
vg0820873126	6.29E-06	3.90E-06	mr1420_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
vg0820873126	NA	1.27E-07	mr1431_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
vg0820873126	6.59E-06	6.59E-06	mr1440_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
vg0820873126	2.01E-06	1.37E-06	mr1467_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
vg0820873126	NA	7.77E-08	mr1488_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
vg0820873126	1.78E-06	1.78E-06	mr1488_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
vg0820873126	NA	1.16E-11	mr1506_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
vg0820873126	5.44E-07	4.89E-07	mr1556_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
vg0820873126	NA	3.06E-57	mr1558_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
vg0820873126	NA	1.66E-33	mr1571_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
vg0820873126	NA	4.24E-08	mr1604_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
vg0820873126	NA	3.61E-08	mr1690_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
vg0820873126	NA	1.75E-15	mr1744_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
vg0820873126	1.50E-06	1.50E-06	mr1747_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
vg0820873126	7.21E-06	6.67E-06	mr1759_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
vg0820873126	5.81E-07	5.81E-07	mr1764_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
vg0820873126	NA	8.52E-06	mr1779_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
vg0820873126	4.44E-07	2.69E-07	mr1823_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
vg0820873126	NA	5.60E-08	mr1824_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
vg0820873126	2.36E-06	1.07E-06	mr1824_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
vg0820873126	5.80E-07	3.45E-07	mr1831_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
vg0820873126	1.80E-06	1.80E-06	mr1840_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
vg0820873126	3.76E-06	2.66E-06	mr1856_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
vg0820873126	NA	2.68E-20	mr1922_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
vg0820873126	NA	9.94E-25	mr1943_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
vg0820873126	NA	6.35E-07	mr1992_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