Search for Variation information by Variation ID:

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

Detailed information for vg0224473315:

Variant ID: vg0224473315 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24473315
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.88, C: 0.13, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GACTGGTAGAAACAGAAGGTAACTCATTGATGAAATTATCATTCTTCACATCCTGAAGGGAGAGCATCTCTCCTAAGGTGCATGTGCTCCTTGGCAATTC[T/C]
ACTTGCTCTTGACTGATCTCATCACAAGTTACAGTTGCCCATCGCTCTGAAAGCCGTTGCTTGGCTTCCTTAGTAACTGATGACTCAGCAAAGTGGGAGA

Reverse complement sequence

TCTCCCACTTTGCTGAGTCATCAGTTACTAAGGAAGCCAAGCAACGGCTTTCAGAGCGATGGGCAACTGTAACTTGTGATGAGATCAGTCAAGAGCAAGT[A/G]
GAATTGCCAAGGAGCACATGCACCTTAGGAGAGATGCTCTCCCTTCAGGATGTGAAGAATGATAATTTCATCAATGAGTTACCTTCTGTTTCTACCAGTC

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	69.70%	28.40%	0.59%	1.29%	NA
All Indica	2759	79.70%	19.30%	0.47%	0.47%	NA
All Japonica	1512	54.50%	41.90%	0.73%	2.84%	NA
Aus	269	59.50%	40.10%	0.37%	0.00%	NA
Indica I	595	89.40%	10.40%	0.17%	0.00%	NA
Indica II	465	70.10%	28.60%	0.86%	0.43%	NA
Indica III	913	80.70%	18.20%	0.44%	0.66%	NA
Indica Intermediate	786	77.00%	21.90%	0.51%	0.64%	NA
Temperate Japonica	767	53.50%	42.40%	0.52%	3.65%	NA
Tropical Japonica	504	58.70%	38.70%	0.60%	1.98%	NA
Japonica Intermediate	241	49.00%	47.30%	1.66%	2.07%	NA
VI/Aromatic	96	51.00%	47.90%	1.04%	0.00%	NA
Intermediate	90	66.70%	25.60%	2.22%	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
vg0224473315	T -> DEL	LOC_Os02g40410.2	N	frameshift_variant	Average:47.027; most accessible tissue: Callus, score: 62.656	N	N	N	N
vg0224473315	T -> DEL	LOC_Os02g40410.1	N	frameshift_variant	Average:47.027; most accessible tissue: Callus, score: 62.656	N	N	N	N
vg0224473315	T -> C	LOC_Os02g40410.1	synonymous_variant ; p.Val468Val; LOW	synonymous_codon	Average:47.027; most accessible tissue: Callus, score: 62.656	N	N	N	N
vg0224473315	T -> C	LOC_Os02g40410.2	synonymous_variant ; p.Val468Val; LOW	synonymous_codon	Average:47.027; most accessible tissue: Callus, score: 62.656	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224473315	8.21E-07	5.48E-06	mr1959_2	Jap_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