Search for Variation information by Variation ID:

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

Detailed information for vg0200620734:

Variant ID: vg0200620734 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 620734
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

GTTTAACTTGACTCCAGCAGCATTGAAGACTTGTTTCCAAGTGTTGGAAGTAAAGAGGCGATCTCTATCACTAATAATAACAGTTGGTAATCCATGTAAT[C/T]
TGTAAAAGTGTGTCTTGAAGAGATCAACAATATGTTCAGAAGTGAAGGGGTGACTTAAGGCAATGAAATGGGCATATTTTGTCAATCTATCGACAATGAC

Reverse complement sequence

GTCATTGTCGATAGATTGACAAAATATGCCCATTTCATTGCCTTAAGTCACCCCTTCACTTCTGAACATATTGTTGATCTCTTCAAGACACACTTTTACA[G/A]
ATTACATGGATTACCAACTGTTATTATTAGTGATAGAGATCGCCTCTTTACTTCCAACACTTGGAAACAAGTCTTCAATGCTGCTGGAGTCAAGTTAAAC

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	44.00%	3.50%	2.01%	50.53%	NA
All Indica	2759	12.40%	5.20%	1.99%	80.39%	NA
All Japonica	1512	95.00%	0.00%	0.40%	4.63%	NA
Aus	269	54.60%	7.80%	11.52%	26.02%	NA
Indica I	595	5.20%	12.90%	3.19%	78.66%	NA
Indica II	465	27.10%	0.20%	1.08%	71.61%	NA
Indica III	913	10.00%	2.60%	1.64%	85.76%	NA
Indica Intermediate	786	12.00%	5.30%	2.04%	80.66%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	90.90%	0.00%	1.19%	7.94%	NA
Japonica Intermediate	241	88.80%	0.00%	0.00%	11.20%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	64.40%	0.00%	3.33%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0200620734	C -> T	LOC_Os02g02100.1	missense_variant ; p.Arg661Lys; MODERATE	nonsynonymous_codon ; R661K	Average:15.079; most accessible tissue: Callus, score: 81.41	unknown	unknown	TOLERATED	1.00
vg0200620734	C -> DEL	LOC_Os02g02100.1	N	frameshift_variant	Average:15.079; most accessible tissue: Callus, score: 81.41	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0200620734	8.22E-06	NA	mr1378	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
vg0200620734	NA	4.59E-07	mr1680	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