Search for Variation information by Variation ID:

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

Detailed information for vg0711712757:

Variant ID: vg0711712757 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11712757
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGAAGTCTTCTGTTCTTGCTTTATTTAATGCCATATCCGATGATCAACTCGAACAGTTCGAGGAGGAGGATTTGGTTTTGCTATCTAACAGATTTTCTC[G/A,T]
AGCTATGAAAAATGTTAGGAACAGGAAAAGAGGAGAACCGAATCGTTGTTTTGAATGTGGAGCACTTGATCATCTTCGTTCACATTGTCCTAAGCTTGGA

Reverse complement sequence

TCCAAGCTTAGGACAATGTGAACGAAGATGATCAAGTGCTCCACATTCAAAACAACGATTCGGTTCTCCTCTTTTCCTGTTCCTAACATTTTTCATAGCT[C/T,A]
GAGAAAATCTGTTAGATAGCAAAACCAAATCCTCCTCCTCGAACTGTTCGAGTTGATCATCGGATATGGCATTAAATAAAGCAAGAACAGAAGACTTCGA

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	90.00%	0.40%	2.98%	6.58%	T: 0.02%
All Indica	2759	94.70%	0.50%	4.02%	0.83%	NA
All Japonica	1512	82.90%	0.20%	1.39%	15.48%	T: 0.07%
Aus	269	97.00%	0.70%	1.12%	1.12%	NA
Indica I	595	88.10%	1.20%	10.42%	0.34%	NA
Indica II	465	97.80%	0.00%	1.94%	0.22%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	91.60%	0.80%	5.09%	2.54%	NA
Temperate Japonica	767	71.30%	0.30%	1.69%	26.73%	NA
Tropical Japonica	504	99.20%	0.20%	0.00%	0.40%	T: 0.20%
Japonica Intermediate	241	85.50%	0.00%	3.32%	11.20%	NA
VI/Aromatic	96	43.80%	1.00%	4.17%	51.04%	NA
Intermediate	90	95.60%	0.00%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711712757	G -> DEL	LOC_Os07g20300.1	N	frameshift_variant	Average:20.766; most accessible tissue: Zhenshan97 young leaf, score: 33.91	N	N	N	N
vg0711712757	G -> A	LOC_Os07g20300.1	missense_variant ; p.Arg95Gln; MODERATE	nonsynonymous_codon ; R95Q	Average:20.766; most accessible tissue: Zhenshan97 young leaf, score: 33.91	benign	0.383	DELETERIOUS	0.04
vg0711712757	G -> T	LOC_Os07g20300.1	missense_variant ; p.Arg95Leu; MODERATE	nonsynonymous_codon ; R95L	Average:20.766; most accessible tissue: Zhenshan97 young leaf, score: 33.91	benign	1.452	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711712757	2.06E-06	2.06E-06	mr1926	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