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Detailed information for vg0522018946:

Variant ID: vg0522018946 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 22018946
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

CCACTACGGTCTGATCGATTTCCTCGAGGGAAAACCAGATTTTTGCCACTTTGATTTTGCAAAGGCAATCTCTCTCTTCTTTTTCTATTTATGAGCTAAT[C/T]
TGAAACAAAAACCAACAATATGTCCATCTTTTCCACAAAAAGAACAAGTATATTTTTCACGATGATTAGACATATTGGTAGCACTAGTAGATTTAGCAAC

Reverse complement sequence

GTTGCTAAATCTACTAGTGCTACCAATATGTCTAATCATCGTGAAAAATATACTTGTTCTTTTTGTGGAAAAGATGGACATATTGTTGGTTTTTGTTTCA[G/A]
ATTAGCTCATAAATAGAAAAAGAAGAGAGAGATTGCCTTTGCAAAATCAAAGTGGCAAAAATCTGGTTTTCCCTCGAGGAAATCGATCAGACCGTAGTGG

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	78.90%	20.70%	0.38%	0.00%	NA
All Indica	2759	65.00%	34.40%	0.65%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	47.40%	50.60%	2.02%	0.00%	NA
Indica II	465	87.70%	12.00%	0.22%	0.00%	NA
Indica III	913	58.40%	41.30%	0.33%	0.00%	NA
Indica Intermediate	786	72.40%	27.40%	0.25%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	0.00%	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
vg0522018946	C -> T	LOC_Os05g37630.1	downstream_gene_variant ; 4089.0bp to feature; MODIFIER	silent_mutation	Average:26.146; most accessible tissue: Zhenshan97 flower, score: 36.732	N	N	N	N
vg0522018946	C -> T	LOC_Os05g37620.1	intron_variant ; MODIFIER	silent_mutation	Average:26.146; most accessible tissue: Zhenshan97 flower, score: 36.732	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0522018946	NA	1.95E-07	mr1044	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
vg0522018946	NA	2.87E-06	mr1044	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
vg0522018946	NA	2.60E-06	mr1115	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
vg0522018946	NA	5.14E-06	mr1418	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
vg0522018946	NA	3.37E-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
vg0522018946	NA	1.96E-07	mr1547	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
vg0522018946	NA	5.88E-06	mr1671	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
vg0522018946	NA	3.32E-06	mr1737	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
vg0522018946	NA	3.86E-06	mr1740	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
vg0522018946	NA	7.13E-08	mr1785	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
vg0522018946	1.99E-06	1.98E-06	mr1856	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
vg0522018946	NA	8.60E-06	mr1856	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
vg0522018946	7.39E-07	NA	mr1992	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
vg0522018946	3.08E-07	3.08E-07	mr1992	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