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Detailed information for vg0328906064:

Variant ID: vg0328906064 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 28906064
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.10, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

GAAGAAGGGATAAAAAAATAAAAAAAATCCATGTCATTGTCCACGTGGCGTGACACGTAGGCAAGACCACAGTCAAACGCGGCTTTGGACCGGGATGATA[C/T]
AATAAACCAAGTTTAGGGACCTCGATGTGCACTTTGTAAGTTCGTGGACCTAAGTGAAACCTCCTGACAAGTTTAAGGATCGCTGGTGTATTTTACTCTT

Reverse complement sequence

AAGAGTAAAATACACCAGCGATCCTTAAACTTGTCAGGAGGTTTCACTTAGGTCCACGAACTTACAAAGTGCACATCGAGGTCCCTAAACTTGGTTTATT[G/A]
TATCATCCCGGTCCAAAGCCGCGTTTGACTGTGGTCTTGCCTACGTGTCACGCCACGTGGACAATGACATGGATTTTTTTTATTTTTTTATCCCTTCTTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.20%	17.20%	1.21%	6.37%	NA
All Indica	2759	68.00%	28.60%	1.01%	2.46%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	7.40%	0.70%	9.67%	82.16%	NA
Indica I	595	91.60%	8.20%	0.17%	0.00%	NA
Indica II	465	41.10%	51.60%	1.94%	5.38%	NA
Indica III	913	66.50%	31.10%	0.55%	1.86%	NA
Indica Intermediate	786	67.70%	27.40%	1.65%	3.31%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	1.00%	2.08%	6.25%	NA
Intermediate	90	74.40%	17.80%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0328906064	C -> T	LOC_Os03g50620.2	downstream_gene_variant ; 1898.0bp to feature; MODIFIER	silent_mutation	Average:53.055; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg0328906064	C -> T	LOC_Os03g50620.1	intron_variant ; MODIFIER	silent_mutation	Average:53.055; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg0328906064	C -> DEL	N	N	silent_mutation	Average:53.055; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0328906064	8.44E-06	2.20E-06	mr1006	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
vg0328906064	NA	3.21E-07	mr1030	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
vg0328906064	NA	2.71E-06	mr1030	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
vg0328906064	NA	2.33E-06	mr1051	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
vg0328906064	NA	2.85E-06	mr1052	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
vg0328906064	NA	6.97E-06	mr1193	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
vg0328906064	NA	7.04E-07	mr1241	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
vg0328906064	NA	5.01E-06	mr1375	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
vg0328906064	1.48E-06	1.48E-06	mr1470	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
vg0328906064	6.64E-07	6.64E-07	mr1488	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
vg0328906064	NA	3.65E-07	mr1536	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
vg0328906064	9.52E-06	9.52E-06	mr1591	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
vg0328906064	NA	3.36E-06	mr1657	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
vg0328906064	NA	1.60E-07	mr1666	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
vg0328906064	NA	4.52E-06	mr1928	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
vg0328906064	NA	7.90E-08	mr1931	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
vg0328906064	NA	7.85E-07	mr1931	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
vg0328906064	NA	6.78E-06	mr1941	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
vg0328906064	NA	1.45E-07	mr1974	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
vg0328906064	NA	1.40E-06	mr1974	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