Search for Variation information by Variation ID:

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

Detailed information for vg0706453758:

Variant ID: vg0706453758 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6453758
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, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTCAAATGCTTCTATCGTTTCAGACTTGCTCAACATAGGGTTAGATCTTGGGGGTTCATGCAGTAAAATTTCAGATTCTATTTTGAGCCTTAGAGAA[G/A]
TAGAAGAAGATAGAATTTCTAAGAGTTTACCCTTGTCGAATTGTTTGTGTAATGAGGTTAACAATAAGGGATTTAGTTCAGAAGGAGAAGAAGAGTTAGA

Reverse complement sequence

TCTAACTCTTCTTCTCCTTCTGAACTAAATCCCTTATTGTTAACCTCATTACACAAACAATTCGACAAGGGTAAACTCTTAGAAATTCTATCTTCTTCTA[C/T]
TTCTCTAAGGCTCAAAATAGAATCTGAAATTTTACTGCATGAACCCCCAAGATCTAACCCTATGTTGAGCAAGTCTGAAACGATAGAAGCATTTGAAAAA

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	91.70%	4.10%	1.65%	2.52%	NA
All Indica	2759	97.00%	0.40%	1.99%	0.65%	NA
All Japonica	1512	87.00%	8.90%	0.79%	3.24%	NA
Aus	269	94.80%	1.10%	2.60%	1.49%	NA
Indica I	595	98.00%	0.00%	1.85%	0.17%	NA
Indica II	465	98.90%	0.00%	0.65%	0.43%	NA
Indica III	913	97.00%	0.30%	2.30%	0.33%	NA
Indica Intermediate	786	94.90%	1.00%	2.54%	1.53%	NA
Temperate Japonica	767	93.50%	5.50%	0.39%	0.65%	NA
Tropical Japonica	504	90.30%	6.50%	0.79%	2.38%	NA
Japonica Intermediate	241	59.80%	24.90%	2.07%	13.28%	NA
VI/Aromatic	96	12.50%	40.60%	3.12%	43.75%	NA
Intermediate	90	86.70%	5.60%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0706453758	G -> DEL	LOC_Os07g11670.1	N	frameshift_variant	Average:65.645; most accessible tissue: Zhenshan97 young leaf, score: 82.982	N	N	N	N
vg0706453758	G -> A	LOC_Os07g11670.1	missense_variant ; p.Val417Ile; MODERATE	nonsynonymous_codon ; V417I	Average:65.645; most accessible tissue: Zhenshan97 young leaf, score: 82.982	unknown	unknown	TOLERATED	0.53

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706453758	6.52E-06	NA	mr1806	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
vg0706453758	NA	6.70E-07	mr1567_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