Search for Variation information by Variation ID:

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

Detailed information for vg0716057799:

Variant ID: vg0716057799 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16057799
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.02, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

TATCGGCTGGAACTACTCCATCGGCTTGTCAGCCGATCGGCTGTTTTGATCTACTATTTGCATATCTTGTCAGTTGCAGGATCAAACTGACTGGCACGCC[C/A]
GCATCTCATTATATTTGGACCTGCACAGGAGCTAAGCAGATCTCCTAGGCCGGTGTGTTCGATTTTTTCGTCAACAAATTGACACATAAATTCTAGCACA

Reverse complement sequence

TGTGCTAGAATTTATGTGTCAATTTGTTGACGAAAAAATCGAACACACCGGCCTAGGAGATCTGCTTAGCTCCTGTGCAGGTCCAAATATAATGAGATGC[G/T]
GGCGTGCCAGTCAGTTTGATCCTGCAACTGACAAGATATGCAAATAGTAGATCAAAACAGCCGATCGGCTGACAAGCCGATGGAGTAGTTCCAGCCGATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.20%	14.30%	0.74%	1.74%	NA
All Indica	2759	73.80%	22.30%	1.23%	2.68%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	77.00%	20.10%	0.37%	2.60%	NA
Indica I	595	61.20%	36.00%	2.02%	0.84%	NA
Indica II	465	87.30%	8.60%	0.86%	3.23%	NA
Indica III	913	78.60%	17.70%	0.88%	2.74%	NA
Indica Intermediate	786	69.70%	25.30%	1.27%	3.69%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0716057799	C -> DEL	N	N	silent_mutation	Average:48.79; most accessible tissue: Minghui63 young leaf, score: 65.92	N	N	N	N
vg0716057799	C -> A	LOC_Os07g27490-LOC_Os07g27500	intergenic_region ; MODIFIER	silent_mutation	Average:48.79; most accessible tissue: Minghui63 young leaf, score: 65.92	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716057799	5.69E-07	7.51E-09	mr1705	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
vg0716057799	NA	3.23E-07	mr1705_2	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