Search for Variation information by Variation ID:

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

Detailed information for vg0608926537:

Variant ID: vg0608926537 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8926537
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

ATCACATATGAAACAACCAATGTTAATGGATTGAAACATATGTTTTTCTTTCATCAAAATATAATCATGTGATATCTTGTTGTAAAGATTTAATTACAAA[G/A]
AATACAACGGTGTGATCGGATCGTAGATTAGATAATTAGTTTAAGAGAAAAATCGTTTTGAAACTAGCTAAAATGCATGCATGCATACATGAGGTGGAGA

Reverse complement sequence

TCTCCACCTCATGTATGCATGCATGCATTTTAGCTAGTTTCAAAACGATTTTTCTCTTAAACTAATTATCTAATCTACGATCCGATCACACCGTTGTATT[C/T]
TTTGTAATTAAATCTTTACAACAAGATATCACATGATTATATTTTGATGAAAGAAAAACATATGTTTCAATCCATTAACATTGGTTGTTTCATATGTGAT

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	80.00%	6.90%	6.77%	6.33%	NA
All Indica	2759	78.70%	3.20%	10.80%	7.36%	NA
All Japonica	1512	83.10%	10.30%	1.32%	5.29%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	74.30%	0.00%	17.65%	8.07%	NA
Indica II	465	97.40%	0.00%	1.29%	1.29%	NA
Indica III	913	64.80%	9.50%	14.46%	11.17%	NA
Indica Intermediate	786	86.90%	0.10%	7.00%	5.98%	NA
Temperate Japonica	767	89.60%	5.60%	1.04%	3.78%	NA
Tropical Japonica	504	81.00%	12.50%	0.40%	6.15%	NA
Japonica Intermediate	241	67.20%	20.30%	4.15%	8.30%	NA
VI/Aromatic	96	9.40%	76.00%	2.08%	12.50%	NA
Intermediate	90	87.80%	7.80%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0608926537	G -> A	LOC_Os06g15740.1	intron_variant ; MODIFIER	silent_mutation	Average:24.056; most accessible tissue: Callus, score: 57.363	N	N	N	N
vg0608926537	G -> DEL	N	N	silent_mutation	Average:24.056; most accessible tissue: Callus, score: 57.363	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608926537	5.66E-06	2.61E-07	mr1020	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
vg0608926537	8.57E-09	8.57E-09	mr1032	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
vg0608926537	2.62E-07	2.62E-07	mr1165	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
vg0608926537	2.04E-08	2.04E-08	mr1478	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
vg0608926537	2.84E-07	1.35E-08	mr1971	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