Search for Variation information by Variation ID:

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

Detailed information for vg0521217382:

Variant ID: vg0521217382 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 21217382
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CAATGGAACGAAATTTGACATTATTTTTTTTAAGATAATAAAATATAATCCTGACCTTTGCTCACAGAATTACAGCTAATTATTAAAAAAAAGTTTCAAA[C/T]
ATAATCACACCTCAAAAGAAGACATAATAGGGACACATCCAAACTGATAGAGACGCACACCGGTACTAACACCAATAGAAAAAAAATAAAACGCACATTT

Reverse complement sequence

AAATGTGCGTTTTATTTTTTTTCTATTGGTGTTAGTACCGGTGTGCGTCTCTATCAGTTTGGATGTGTCCCTATTATGTCTTCTTTTGAGGTGTGATTAT[G/A]
TTTGAAACTTTTTTTTAATAATTAGCTGTAATTCTGTGAGCAAAGGTCAGGATTATATTTTATTATCTTAAAAAAAATAATGTCAAATTTCGTTCCATTG

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	83.40%	13.90%	2.77%	0.00%	NA
All Indica	2759	72.30%	23.20%	4.57%	0.00%	NA
All Japonica	1512	99.50%	0.40%	0.07%	0.00%	NA
Aus	269	98.90%	0.40%	0.74%	0.00%	NA
Indica I	595	89.90%	2.50%	7.56%	0.00%	NA
Indica II	465	64.30%	29.00%	6.67%	0.00%	NA
Indica III	913	67.00%	31.50%	1.42%	0.00%	NA
Indica Intermediate	786	69.70%	25.60%	4.71%	0.00%	NA
Temperate Japonica	767	99.20%	0.70%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	10.00%	2.22%	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
vg0521217382	C -> T	LOC_Os05g35730.1	upstream_gene_variant ; 2951.0bp to feature; MODIFIER	silent_mutation	Average:56.125; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N
vg0521217382	C -> T	LOC_Os05g35740.1	upstream_gene_variant ; 450.0bp to feature; MODIFIER	silent_mutation	Average:56.125; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N
vg0521217382	C -> T	LOC_Os05g35750.1	upstream_gene_variant ; 1737.0bp to feature; MODIFIER	silent_mutation	Average:56.125; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N
vg0521217382	C -> T	LOC_Os05g35730.2	upstream_gene_variant ; 2951.0bp to feature; MODIFIER	silent_mutation	Average:56.125; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N
vg0521217382	C -> T	LOC_Os05g35740.2	upstream_gene_variant ; 450.0bp to feature; MODIFIER	silent_mutation	Average:56.125; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N
vg0521217382	C -> T	LOC_Os05g35740.3	upstream_gene_variant ; 450.0bp to feature; MODIFIER	silent_mutation	Average:56.125; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N
vg0521217382	C -> T	LOC_Os05g35740-LOC_Os05g35750	intergenic_region ; MODIFIER	silent_mutation	Average:56.125; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0521217382	NA	3.68E-07	mr1399	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
vg0521217382	NA	4.14E-06	mr1564	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
vg0521217382	5.96E-06	7.40E-07	mr1564	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