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Detailed information for vg0223051444:

Variant ID: vg0223051444 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23051444
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.89, G: 0.11, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

GAATATAGATACTGTTTACACATTTGGCCGGCCTTTGCATGGCGCACAGTTGAAGAATGACAAGAGAAAATAAGATGAAGAGAGAGATCAACGGGACTAC[A/G]
TATCCCACCGTCTACAATAATAATATCTTAATTTGAATAGGAATTTTTTTCACCTGAGCTTATTTATCTATACACAAATGGAGGGGAGCTGCCATATCTA

Reverse complement sequence

TAGATATGGCAGCTCCCCTCCATTTGTGTATAGATAAATAAGCTCAGGTGAAAAAAATTCCTATTCAAATTAAGATATTATTATTGTAGACGGTGGGATA[T/C]
GTAGTCCCGTTGATCTCTCTCTTCATCTTATTTTCTCTTGTCATTCTTCAACTGTGCGCCATGCAAAGGCCGGCCAAATGTGTAAACAGTATCTATATTC

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	53.00%	46.70%	0.34%	0.00%	NA
All Indica	2759	21.50%	78.00%	0.54%	0.00%	NA
All Japonica	1512	98.70%	1.30%	0.00%	0.00%	NA
Aus	269	96.70%	3.00%	0.37%	0.00%	NA
Indica I	595	21.70%	77.80%	0.50%	0.00%	NA
Indica II	465	31.40%	68.40%	0.22%	0.00%	NA
Indica III	913	17.10%	82.50%	0.44%	0.00%	NA
Indica Intermediate	786	20.60%	78.50%	0.89%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	97.60%	2.40%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	68.90%	31.10%	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
vg0223051444	A -> G	LOC_Os02g38120.1	downstream_gene_variant ; 4048.0bp to feature; MODIFIER	silent_mutation	Average:57.033; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N
vg0223051444	A -> G	LOC_Os02g38120-LOC_Os02g38130	intergenic_region ; MODIFIER	silent_mutation	Average:57.033; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223051444	2.14E-06	NA	mr1067	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
vg0223051444	1.92E-06	NA	mr1067	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
vg0223051444	NA	1.40E-19	mr1077	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
vg0223051444	NA	7.28E-06	mr1077	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
vg0223051444	NA	5.92E-30	mr1237	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
vg0223051444	NA	4.75E-15	mr1592	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
vg0223051444	NA	2.80E-11	mr1609	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
vg0223051444	8.19E-06	NA	mr1918	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
vg0223051444	5.31E-07	NA	mr1918	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
vg0223051444	1.92E-08	NA	mr1067_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
vg0223051444	4.83E-08	NA	mr1067_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
vg0223051444	2.41E-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
vg0223051444	3.31E-06	NA	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
vg0223051444	5.66E-06	9.84E-17	mr1592_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
vg0223051444	6.26E-06	NA	mr1918_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
vg0223051444	1.34E-06	NA	mr1918_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
vg0223051444	NA	7.19E-07	mr1925_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
vg0223051444	4.16E-07	NA	mr1929_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
vg0223051444	1.31E-06	9.88E-06	mr1929_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
vg0223051444	4.39E-06	NA	mr1962_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
vg0223051444	6.33E-06	NA	mr1962_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