Search for Variation information by Variation ID:

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

Detailed information for vg0708109465:

Variant ID: vg0708109465 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 8109465
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.02, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

TCTAACATAAACACTGAAGTATAAAGTGGGACATGGCTTTGGGCCAAGTGCACTTCTTGTGCTAGCTGAGCCAACCTAGTCAAGATAAAAGAAGGGACCG[A/G]
GAGGGTATACATGTGAAAGGAATAAGTCTATTTTACCTCCCTCATCTCTTGCTCGTAATTGAAACGCTTCCTTCAAACATCGATTTGTACCCATTTCGAA

Reverse complement sequence

TTCGAAATGGGTACAAATCGATGTTTGAAGGAAGCGTTTCAATTACGAGCAAGAGATGAGGGAGGTAAAATAGACTTATTCCTTTCACATGTATACCCTC[T/C]
CGGTCCCTTCTTTTATCTTGACTAGGTTGGCTCAGCTAGCACAAGAAGTGCACTTGGCCCAAAGCCATGTCCCACTTTATACTTCAGTGTTTATGTTAGA

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	40.10%	19.70%	0.78%	39.46%	NA
All Indica	2759	38.40%	1.30%	0.87%	59.41%	NA
All Japonica	1512	30.70%	57.10%	0.66%	11.57%	NA
Aus	269	95.90%	1.50%	0.74%	1.86%	NA
Indica I	595	9.20%	0.70%	2.69%	87.39%	NA
Indica II	465	66.50%	3.40%	0.22%	29.89%	NA
Indica III	913	45.00%	0.40%	0.33%	54.22%	NA
Indica Intermediate	786	36.10%	1.70%	0.51%	61.70%	NA
Temperate Japonica	767	5.90%	79.10%	0.39%	14.60%	NA
Tropical Japonica	504	68.10%	20.80%	0.40%	10.71%	NA
Japonica Intermediate	241	31.50%	62.70%	2.07%	3.73%	NA
VI/Aromatic	96	79.20%	0.00%	0.00%	20.83%	NA
Intermediate	90	42.20%	27.80%	1.11%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0708109465	A -> DEL	N	N	silent_mutation	Average:14.261; most accessible tissue: Callus, score: 95.217	N	N	N	N
vg0708109465	A -> G	LOC_Os07g14220.1	upstream_gene_variant ; 4233.0bp to feature; MODIFIER	silent_mutation	Average:14.261; most accessible tissue: Callus, score: 95.217	N	N	N	N
vg0708109465	A -> G	LOC_Os07g14230.1	upstream_gene_variant ; 715.0bp to feature; MODIFIER	silent_mutation	Average:14.261; most accessible tissue: Callus, score: 95.217	N	N	N	N
vg0708109465	A -> G	LOC_Os07g14230-LOC_Os07g14240	intergenic_region ; MODIFIER	silent_mutation	Average:14.261; most accessible tissue: Callus, score: 95.217	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0708109465	NA	6.28E-06	mr1112_2	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
vg0708109465	NA	7.28E-07	mr1423_2	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
vg0708109465	NA	3.84E-06	mr1588_2	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
vg0708109465	3.61E-06	NA	mr1680_2	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
vg0708109465	NA	1.60E-11	mr1789_2	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
vg0708109465	NA	7.24E-06	mr1844_2	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