Search for Variation information by Variation ID:

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

Detailed information for vg0420181217:

Variant ID: vg0420181217 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 20181217
Reference Allele: C	Alternative Allele: T,G
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 168. )

Flanking Sequence (100 bp) in Reference Genome:

AACCATTTTTCAAAAGAAAATCTCGGAGACATTCATACCAAGCTCTAGGGGCTTGTTTGAGCCCATAGAGCGCCTTGTGGAGCTTGTACACATGGTTTGG[C/T,G]
AACTTTGGATCCTCAAACCCTGGTGGTTGCTCCACATAGACCAACTCCGAGATAGGTCCATTGAGAAAGGCACTCTTGACATCCATTTGGAACAACCTGA

Reverse complement sequence

TCAGGTTGTTCCAAATGGATGTCAAGAGTGCCTTTCTCAATGGACCTATCTCGGAGTTGGTCTATGTGGAGCAACCACCAGGGTTTGAGGATCCAAAGTT[G/A,C]
CCAAACCATGTGTACAAGCTCCACAAGGCGCTCTATGGGCTCAAACAAGCCCCTAGAGCTTGGTATGAATGTCTCCGAGATTTTCTTTTGAAAAATGGTT

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	42.90%	40.80%	12.06%	4.27%	NA
All Indica	2759	66.80%	6.60%	19.75%	6.89%	NA
All Japonica	1512	0.40%	99.50%	0.07%	0.07%	NA
Aus	269	55.00%	36.40%	6.32%	2.23%	NA
Indica I	595	64.00%	3.70%	26.39%	5.88%	NA
Indica II	465	54.00%	9.20%	25.16%	11.61%	NA
Indica III	913	73.20%	4.70%	16.21%	5.91%	NA
Indica Intermediate	786	69.10%	9.30%	15.65%	5.98%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.00%	0.20%	0.00%	NA
Japonica Intermediate	241	0.00%	99.60%	0.00%	0.41%	NA
VI/Aromatic	96	16.70%	83.30%	0.00%	0.00%	NA
Intermediate	90	16.70%	70.00%	7.78%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0420181217	C -> DEL	N	N	silent_mutation	Average:25.841; most accessible tissue: Minghui63 root, score: 45.031	N	N	N	N
vg0420181217	C -> G	LOC_Os04g33390-LOC_Os04g33330	intergenic_region ; MODIFIER	N	Average:25.841; most accessible tissue: Minghui63 root, score: 45.031	N	N	N	N
vg0420181217	C -> T	LOC_Os04g33390-LOC_Os04g33330	intergenic_region ; MODIFIER	silent_mutation	Average:25.841; most accessible tissue: Minghui63 root, score: 45.031	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0420181217	5.26E-06	NA	mr1350_2	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
vg0420181217	NA	8.55E-11	mr1537_2	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
vg0420181217	NA	2.05E-07	mr1804_2	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