Search for Variation information by Variation ID:

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

Detailed information for vg0627335333:

Variant ID: vg0627335333 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 27335333
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCATCGCCGTCTGGTTAACCTTCCCTAGTATTATACATTTTTTATCCAAATGATCAAAATACTCCTGGAACAAAAACATCCAAAATTTGGACAAAAATTT[C/T]
GAAATATCAATATTATAAACATAAGATTGTAAACATCCAATTTTTGTCAAAAACTTAAAATATGATAATTCAGAATTTTTTTATCAAACTTTAGAAGTTT

Reverse complement sequence

AAACTTCTAAAGTTTGATAAAAAAATTCTGAATTATCATATTTTAAGTTTTTGACAAAAATTGGATGTTTACAATCTTATGTTTATAATATTGATATTTC[G/A]
AAATTTTTGTCCAAATTTTGGATGTTTTTGTTCCAGGAGTATTTTGATCATTTGGATAAAAAATGTATAATACTAGGGAAGGTTAACCAGACGGCGATGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.30%	8.40%	0.32%	0.00%	NA
All Indica	2759	94.80%	5.10%	0.07%	0.00%	NA
All Japonica	1512	92.10%	7.10%	0.79%	0.00%	NA
Aus	269	48.00%	52.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.40%	2.60%	0.00%	0.00%	NA
Indica III	913	89.90%	10.00%	0.11%	0.00%	NA
Indica Intermediate	786	95.00%	4.80%	0.13%	0.00%	NA
Temperate Japonica	767	98.40%	1.30%	0.26%	0.00%	NA
Tropical Japonica	504	84.50%	13.90%	1.59%	0.00%	NA
Japonica Intermediate	241	88.00%	11.20%	0.83%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0627335333	C -> T	LOC_Os06g45210.1	upstream_gene_variant ; 4977.0bp to feature; MODIFIER	silent_mutation	Average:39.514; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0627335333	C -> T	LOC_Os06g45230.1	upstream_gene_variant ; 1266.0bp to feature; MODIFIER	silent_mutation	Average:39.514; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0627335333	C -> T	LOC_Os06g45220.1	downstream_gene_variant ; 2485.0bp to feature; MODIFIER	silent_mutation	Average:39.514; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0627335333	C -> T	LOC_Os06g45240.1	downstream_gene_variant ; 514.0bp to feature; MODIFIER	silent_mutation	Average:39.514; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0627335333	C -> T	LOC_Os06g45230-LOC_Os06g45240	intergenic_region ; MODIFIER	silent_mutation	Average:39.514; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0627335333	4.18E-07	4.17E-07	mr1978	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