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Detailed information for vg0420602297:

Variant ID: vg0420602297 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 20602297
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, G: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTCCTCATTTTTAAAATATACGACGTTTTTTTACTTCTCGCATAATGCTTTACTATTCGTCTTATTAAAAATTAGTATAAATACGTAAAAGTATTAGT[G/T]
AAGATTATATATCATCTGATGATAAAACAAATCATAACGAAATAAATGAAATTCATGCAAACTTTTTAAATAAAAAGAATGGTCAAACGGCTCAAATATT

Reverse complement sequence

AATATTTGAGCCGTTTGACCATTCTTTTTATTTAAAAAGTTTGCATGAATTTCATTTATTTCGTTATGATTTGTTTTATCATCAGATGATATATAATCTT[C/A]
ACTAATACTTTTACGTATTTATACTAATTTTTAATAAGACGAATAGTAAAGCATTATGCGAGAAGTAAAAAAACGTCGTATATTTTAAAAATGAGGAAGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.80%	24.00%	0.28%	0.00%	NA
All Indica	2759	98.20%	1.50%	0.25%	0.00%	NA
All Japonica	1512	29.80%	69.90%	0.26%	0.00%	NA
Aus	269	98.90%	0.40%	0.74%	0.00%	NA
Indica I	595	98.30%	0.50%	1.18%	0.00%	NA
Indica II	465	95.70%	4.30%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	98.10%	1.90%	0.00%	0.00%	NA
Temperate Japonica	767	7.80%	91.90%	0.26%	0.00%	NA
Tropical Japonica	504	57.90%	42.10%	0.00%	0.00%	NA
Japonica Intermediate	241	41.10%	58.10%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	64.40%	35.60%	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
vg0420602297	G -> T	LOC_Os04g34020.1	downstream_gene_variant ; 4245.0bp to feature; MODIFIER	silent_mutation	Average:36.577; most accessible tissue: Callus, score: 72.393	N	N	N	N
vg0420602297	G -> T	LOC_Os04g34010-LOC_Os04g34020	intergenic_region ; MODIFIER	silent_mutation	Average:36.577; most accessible tissue: Callus, score: 72.393	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0420602297	NA	8.67E-06	mr1277	Jap_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
vg0420602297	NA	5.94E-13	mr1740	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
vg0420602297	NA	5.62E-07	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
vg0420602297	NA	1.22E-12	mr1853	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
vg0420602297	NA	1.08E-14	mr1277_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
vg0420602297	NA	2.37E-08	mr1399_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
vg0420602297	NA	5.76E-07	mr1554_2	Jap_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
vg0420602297	NA	2.24E-08	mr1662_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
vg0420602297	NA	6.45E-17	mr1730_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
vg0420602297	NA	1.77E-16	mr1790_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
vg0420602297	NA	4.56E-46	mr1805_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
vg0420602297	NA	2.10E-08	mr1805_2	Jap_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
vg0420602297	NA	8.15E-13	mr1853_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