Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0825505240:

Variant ID: vg0825505240 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25505240
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

AAACAAAGCTCTTTTTTTTTTATCAATTTTTCTCATTGTCATATTTTTGCTTGATAAAACCATGAGGTACAAACTCCCTCTCAAACCATGCCAAAAGGAT[G/A]
AATTATTCCCAATTCACCACGAAGAAAAGCAAAGCGATTAGAATCCAAAGGTTTAGTGAAAATATCATCAATTTACAACTTTGTGTCCAAAAACTGCAAT

Reverse complement sequence

ATTGCAGTTTTTGGACACAAAGTTGTAAATTGATGATATTTTCACTAAACCTTTGGATTCTAATCGCTTTGCTTTTCTTCGTGGTGAATTGGGAATAATT[C/T]
ATCCTTTTGGCATGGTTTGAGAGGGAGTTTGTACCTCATGGTTTTATCAAGCAAAAATATGACAATGAGAAAAATTGATAAAAAAAAAAGAGCTTTGTTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.40%	18.00%	9.20%	3.34%	NA
All Indica	2759	57.80%	22.40%	14.06%	5.69%	NA
All Japonica	1512	99.30%	0.40%	0.33%	0.00%	NA
Aus	269	14.50%	74.00%	11.52%	0.00%	NA
Indica I	595	81.30%	8.10%	9.41%	1.18%	NA
Indica II	465	75.90%	13.30%	8.82%	1.94%	NA
Indica III	913	29.00%	39.10%	20.04%	11.83%	NA
Indica Intermediate	786	62.80%	19.20%	13.74%	4.20%	NA
Temperate Japonica	767	99.60%	0.30%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	97.90%	0.80%	1.24%	0.00%	NA
VI/Aromatic	96	83.30%	9.40%	7.29%	0.00%	NA
Intermediate	90	72.20%	22.20%	4.44%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0825505240	G -> A	LOC_Os08g40280.1	downstream_gene_variant ; 3079.0bp to feature; MODIFIER	silent_mutation	Average:15.585; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0825505240	G -> A	LOC_Os08g40290.1	downstream_gene_variant ; 73.0bp to feature; MODIFIER	silent_mutation	Average:15.585; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0825505240	G -> A	LOC_Os08g40280-LOC_Os08g40290	intergenic_region ; MODIFIER	silent_mutation	Average:15.585; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0825505240	G -> DEL	N	N	silent_mutation	Average:15.585; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825505240	NA	5.75E-06	mr1193	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
vg0825505240	1.31E-06	2.17E-06	mr1397	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