Search for Variation information by Variation ID:

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

Detailed information for vg0911094465:

Variant ID: vg0911094465 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11094465
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAACCTTCTTCGAAGGAATCGCTTCTACCCACTTGCTAAAATAATCAGTCGCCACCAATATAAACTTATGCCCTTTACTCAATGGTGGATTAATCATGCC[G/A]
ATTATATCAATTCCCCAACCTCTAAATGGCCATGGCTTAATGATGGGATTCATAGCCGACGCCGATGCCCTCTGGATCGCCCCAAATTTCTTACAATCTT

Reverse complement sequence

AAGATTGTAAGAAATTTGGGGCGATCCAGAGGGCATCGGCGTCGGCTATGAATCCCATCATTAAGCCATGGCCATTTAGAGGTTGGGGAATTGATATAAT[C/T]
GGCATGATTAATCCACCATTGAGTAAAGGGCATAAGTTTATATTGGTGGCGACTGATTATTTTAGCAAGTGGGTAGAAGCGATTCCTTCGAAGAAGGTTG

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	62.30%	5.10%	8.00%	24.63%	NA
All Indica	2759	61.60%	0.40%	7.14%	30.88%	NA
All Japonica	1512	73.00%	14.60%	2.58%	9.79%	NA
Aus	269	19.30%	0.00%	32.34%	48.33%	NA
Indica I	595	83.70%	0.00%	1.51%	14.79%	NA
Indica II	465	40.00%	0.90%	5.81%	53.33%	NA
Indica III	913	59.80%	0.10%	10.30%	29.79%	NA
Indica Intermediate	786	59.70%	0.80%	8.52%	31.04%	NA
Temperate Japonica	767	86.80%	0.90%	1.17%	11.08%	NA
Tropical Japonica	504	48.20%	40.90%	3.17%	7.74%	NA
Japonica Intermediate	241	80.90%	3.30%	5.81%	9.96%	NA
VI/Aromatic	96	38.50%	0.00%	48.96%	12.50%	NA
Intermediate	90	55.60%	11.10%	8.89%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0911094465	G -> DEL	LOC_Os09g18100.1	N	frameshift_variant	Average:38.623; most accessible tissue: Zhenshan97 young leaf, score: 50.669	N	N	N	N
vg0911094465	G -> A	LOC_Os09g18100.1	synonymous_variant ; p.Ile800Ile; LOW	synonymous_codon	Average:38.623; most accessible tissue: Zhenshan97 young leaf, score: 50.669	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911094465	4.83E-07	4.83E-07	mr1848	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