Search for Variation information by Variation ID:

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

Detailed information for vg0818177422:

Variant ID: vg0818177422 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18177422
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

TTGTCAAAATGGCGAATTGGAGGCGAAGACATCCTGGTCGAACCTTAGAGGATTACGACCGGTGCCACATCTAGCGCCGCGATGACATTGCCACACTTTG[A/G]
TTAGACTTCGAAATGACTAATCGTCGAGCTGCTATCGCTTGACGTCGGTGTGTATTTCGCCTCCTTCCCCCCTTAAAGTCGTGTACAGTATAGATGACGA

Reverse complement sequence

TCGTCATCTATACTGTACACGACTTTAAGGGGGGAAGGAGGCGAAATACACACCGACGTCAAGCGATAGCAGCTCGACGATTAGTCATTTCGAAGTCTAA[T/C]
CAAAGTGTGGCAATGTCATCGCGGCGCTAGATGTGGCACCGGTCGTAATCCTCTAAGGTTCGACCAGGATGTCTTCGCCTCCAATTCGCCATTTTGACAA

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	86.70%	5.90%	4.89%	2.50%	NA
All Indica	2759	87.20%	3.30%	5.36%	4.17%	NA
All Japonica	1512	87.90%	7.70%	4.23%	0.20%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	73.40%	1.20%	10.59%	14.79%	NA
Indica II	465	95.90%	1.90%	1.51%	0.65%	NA
Indica III	913	88.80%	6.10%	4.38%	0.66%	NA
Indica Intermediate	786	90.60%	2.30%	4.83%	2.29%	NA
Temperate Japonica	767	88.70%	9.60%	1.69%	0.00%	NA
Tropical Japonica	504	93.50%	0.80%	5.16%	0.60%	NA
Japonica Intermediate	241	73.90%	15.80%	10.37%	0.00%	NA
VI/Aromatic	96	20.80%	65.60%	13.54%	0.00%	NA
Intermediate	90	84.40%	8.90%	6.67%	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
vg0818177422	A -> G	LOC_Os08g29630.1	downstream_gene_variant ; 3212.0bp to feature; MODIFIER	silent_mutation	Average:39.861; most accessible tissue: Minghui63 flag leaf, score: 52.137	N	N	N	N
vg0818177422	A -> G	LOC_Os08g29615-LOC_Os08g29630	intergenic_region ; MODIFIER	silent_mutation	Average:39.861; most accessible tissue: Minghui63 flag leaf, score: 52.137	N	N	N	N
vg0818177422	A -> DEL	N	N	silent_mutation	Average:39.861; most accessible tissue: Minghui63 flag leaf, score: 52.137	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818177422	NA	2.70E-06	mr1239	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
vg0818177422	1.88E-07	1.88E-07	mr1986	Jap_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