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Detailed information for vg0225999747:

Variant ID: vg0225999747 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 25999747
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:

AACAAATAAAAAATCTGAATTATATGAACGATTTTCTGTTTACCCCATTCAAATCAACCGGCTTAATTAAATTATATTGTCTAGAAATTGAGAAAAAGTC[G/T]
CATTGAATTTTATTGCAAGAACTTGAGAAAGAAAATCGTTCTCCCGTAAATAAACACTGCTAATACGGTTGAAACAAGATACTCCCTCCGTCCCATAATA

Reverse complement sequence

TATTATGGGACGGAGGGAGTATCTTGTTTCAACCGTATTAGCAGTGTTTATTTACGGGAGAACGATTTTCTTTCTCAAGTTCTTGCAATAAAATTCAATG[C/A]
GACTTTTTCTCAATTTCTAGACAATATAATTTAATTAAGCCGGTTGATTTGAATGGGGTAAACAGAAAATCGTTCATATAATTCAGATTTTTTATTTGTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.30%	3.90%	0.80%	0.00%	NA
All Indica	2759	92.10%	6.60%	1.27%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	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	74.40%	21.70%	3.87%	0.00%	NA
Indica III	913	99.00%	0.80%	0.22%	0.00%	NA
Indica Intermediate	786	88.50%	9.50%	1.91%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	3.30%	3.33%	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
vg0225999747	G -> T	LOC_Os02g43150.1	downstream_gene_variant ; 571.0bp to feature; MODIFIER	silent_mutation	Average:45.315; most accessible tissue: Callus, score: 71.622	N	N	N	N
vg0225999747	G -> T	LOC_Os02g43150.2	downstream_gene_variant ; 571.0bp to feature; MODIFIER	silent_mutation	Average:45.315; most accessible tissue: Callus, score: 71.622	N	N	N	N
vg0225999747	G -> T	LOC_Os02g43150-LOC_Os02g43160	intergenic_region ; MODIFIER	silent_mutation	Average:45.315; most accessible tissue: Callus, score: 71.622	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0225999747	NA	2.33E-06	mr1074	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
vg0225999747	NA	2.34E-06	mr1130	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
vg0225999747	2.49E-06	NA	mr1072_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
vg0225999747	6.67E-06	2.01E-09	mr1072_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
vg0225999747	5.57E-06	NA	mr1075_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
vg0225999747	NA	1.17E-09	mr1075_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
vg0225999747	NA	1.15E-09	mr1077_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
vg0225999747	4.12E-07	NA	mr1124_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
vg0225999747	1.93E-07	3.62E-09	mr1124_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
vg0225999747	NA	4.48E-08	mr1149_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
vg0225999747	NA	1.13E-08	mr1441_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
vg0225999747	NA	1.77E-07	mr1497_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
vg0225999747	NA	9.85E-06	mr1497_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
vg0225999747	NA	5.93E-06	mr1592_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
vg0225999747	8.36E-06	NA	mr1861_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
vg0225999747	NA	5.11E-10	mr1861_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
vg0225999747	NA	6.63E-06	mr1946_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
vg0225999747	NA	6.63E-06	mr1948_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