Search for Variation information by Variation ID:

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

Detailed information for vg0817358646:

Variant ID: vg0817358646 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17358646
Reference Allele: T	Alternative Allele: G,C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.32, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

CGCCAAAATCAGCATCGGAATATCCACTTAAGCATATAGAAGATGAAGTAGAATACCAAATTCCAAACTCGAGTGTATGATTCAAATACCTCATTATTCG[T/G,C]
TTGACCGCTTGACGATGTGAAGCATGAGGAGAAGCTTGAAAGCGTGCAGACAAACACACAGCAAACTGTATGTCTAGCCTAGAAGCAGTTAGATACAACA

Reverse complement sequence

TGTTGTATCTAACTGCTTCTAGGCTAGACATACAGTTTGCTGTGTGTTTGTCTGCACGCTTTCAAGCTTCTCCTCATGCTTCACATCGTCAAGCGGTCAA[A/C,G]
CGAATAATGAGGTATTTGAATCATACACTCGAGTTTGGAATTTGGTATTCTACTTCATCTTCTATATGCTTAAGTGGATATTCCGATGCTGATTTTGGCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.00%	6.70%	1.44%	55.67%	G: 0.21%
All Indica	2759	4.70%	7.60%	2.25%	85.14%	G: 0.36%
All Japonica	1512	94.20%	2.00%	0.00%	3.84%	NA
Aus	269	1.90%	27.90%	1.86%	68.40%	NA
Indica I	595	8.20%	3.20%	0.84%	87.56%	G: 0.17%
Indica II	465	4.50%	7.30%	1.94%	85.38%	G: 0.86%
Indica III	913	1.80%	14.10%	2.74%	81.27%	G: 0.11%
Indica Intermediate	786	5.50%	3.40%	2.93%	87.66%	G: 0.51%
Temperate Japonica	767	95.40%	3.70%	0.00%	0.91%	NA
Tropical Japonica	504	90.90%	0.20%	0.00%	8.93%	NA
Japonica Intermediate	241	97.10%	0.40%	0.00%	2.49%	NA
VI/Aromatic	96	92.70%	0.00%	0.00%	7.29%	NA
Intermediate	90	57.80%	4.40%	1.11%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817358646	T -> G	LOC_Os08g28450.1	downstream_gene_variant ; 1126.0bp to feature; MODIFIER	silent_mutation	Average:6.94; most accessible tissue: Callus, score: 17.861	N	N	N	N
vg0817358646	T -> G	LOC_Os08g28430-LOC_Os08g28450	intergenic_region ; MODIFIER	silent_mutation	Average:6.94; most accessible tissue: Callus, score: 17.861	N	N	N	N
vg0817358646	T -> C	LOC_Os08g28450.1	downstream_gene_variant ; 1126.0bp to feature; MODIFIER	silent_mutation	Average:6.94; most accessible tissue: Callus, score: 17.861	N	N	N	N
vg0817358646	T -> C	LOC_Os08g28430-LOC_Os08g28450	intergenic_region ; MODIFIER	silent_mutation	Average:6.94; most accessible tissue: Callus, score: 17.861	N	N	N	N
vg0817358646	T -> DEL	N	N	silent_mutation	Average:6.94; most accessible tissue: Callus, score: 17.861	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817358646	1.58E-06	NA	mr1040	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
vg0817358646	4.47E-06	4.47E-06	mr1040	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