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Detailed information for vg0625068800:

Variant ID: vg0625068800 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 25068800
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.60, G: 0.40, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

AAACTAATTACACAGTGTGCGTGTAAATTGCGAGATGAATCTTTTAAGCCTAATTGCACCATGATTTAACAATGTGGTGCTACAGTAAACATTTACTAAT[A/G]
ACGAATTAATTAGGCTTAATAAATTTGTCTCGCAGTTTCCTAGCGAAATCTGTAATTTGTTTTGTTATTAGACTACGTTTAGTATTTCAAATGTGTGTCC

Reverse complement sequence

GGACACACATTTGAAATACTAAACGTAGTCTAATAACAAAACAAATTACAGATTTCGCTAGGAAACTGCGAGACAAATTTATTAAGCCTAATTAATTCGT[T/C]
ATTAGTAAATGTTTACTGTAGCACCACATTGTTAAATCATGGTGCAATTAGGCTTAAAAGATTCATCTCGCAATTTACACGCACACTGTGTAATTAGTTT

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	73.60%	26.10%	0.28%	0.00%	NA
All Indica	2759	96.90%	3.00%	0.04%	0.00%	NA
All Japonica	1512	32.30%	67.30%	0.33%	0.00%	NA
Aus	269	90.70%	8.90%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	95.10%	4.90%	0.00%	0.00%	NA
Indica III	913	98.80%	1.20%	0.00%	0.00%	NA
Indica Intermediate	786	93.50%	6.40%	0.13%	0.00%	NA
Temperate Japonica	767	50.10%	49.40%	0.52%	0.00%	NA
Tropical Japonica	504	12.30%	87.70%	0.00%	0.00%	NA
Japonica Intermediate	241	17.80%	81.70%	0.41%	0.00%	NA
VI/Aromatic	96	19.80%	79.20%	1.04%	0.00%	NA
Intermediate	90	60.00%	34.40%	5.56%	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
vg0625068800	A -> G	LOC_Os06g41810.1	downstream_gene_variant ; 4742.0bp to feature; MODIFIER	silent_mutation	Average:27.877; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0625068800	A -> G	LOC_Os06g41800.1	intron_variant ; MODIFIER	silent_mutation	Average:27.877; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0625068800	NA	5.42E-07	mr1103	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
vg0625068800	NA	1.33E-06	mr1123	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
vg0625068800	NA	3.62E-06	mr1124	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
vg0625068800	NA	2.75E-07	mr1226	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
vg0625068800	NA	9.51E-07	mr1411	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
vg0625068800	1.13E-06	6.56E-10	mr1805	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
vg0625068800	NA	5.08E-07	mr1886	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
vg0625068800	NA	8.75E-08	mr1548_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
vg0625068800	NA	1.10E-08	mr1600_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