Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0706623517:

Variant ID: vg0706623517 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6623517
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTATTTTAAAAAGAACCATTCATTGCTAGCTTAATTTGGTGGCAATAAATATCTCTGCTGCCAACAATATACACAATATAAAGAGAGTGCCCTCTCCC[C/T]
GGTCACATTGCCAAACCATGACTTCACAAGCCCTCATATATCATTGCCTCATTGTTCAGCTCCTTCTGCTCCGAGCTCTTATGTCACAGTGAACTGATGT

Reverse complement sequence

ACATCAGTTCACTGTGACATAAGAGCTCGGAGCAGAAGGAGCTGAACAATGAGGCAATGATATATGAGGGCTTGTGAAGTCATGGTTTGGCAATGTGACC[G/A]
GGGAGAGGGCACTCTCTTTATATTGTGTATATTGTTGGCAGCAGAGATATTTATTGCCACCAAATTAAGCTAGCAATGAATGGTTCTTTTTAAAATAAAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.30%	15.20%	1.38%	43.14%	NA
All Indica	2759	11.60%	18.50%	1.59%	68.36%	NA
All Japonica	1512	93.10%	0.10%	0.20%	6.55%	NA
Aus	269	11.50%	69.90%	6.32%	12.27%	NA
Indica I	595	16.60%	20.00%	2.35%	61.01%	NA
Indica II	465	13.50%	4.30%	0.43%	81.72%	NA
Indica III	913	4.20%	21.10%	1.53%	73.17%	NA
Indica Intermediate	786	15.10%	22.60%	1.78%	60.43%	NA
Temperate Japonica	767	87.70%	0.10%	0.39%	11.73%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	97.10%	0.40%	0.00%	2.49%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	62.20%	13.30%	1.11%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0706623517	C -> DEL	N	N	silent_mutation	Average:12.269; most accessible tissue: Callus, score: 78.69	N	N	N	N
vg0706623517	C -> T	LOC_Os07g11920-LOC_Os07g11970	intergenic_region ; MODIFIER	silent_mutation	Average:12.269; most accessible tissue: Callus, score: 78.69	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706623517	8.94E-06	8.94E-06	mr1501	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
vg0706623517	3.70E-06	3.70E-06	mr1656	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
vg0706623517	7.14E-06	7.14E-06	mr1802	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