Search for Variation information by Variation ID:

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

Detailed information for vg0220739288:

Variant ID: vg0220739288 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20739288
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 350. )

Flanking Sequence (100 bp) in Reference Genome:

CAGCTTCTGAGTCACATCCCTGCATACACTTGGTGAACAGCTTATTAAATGCTTTGGAACCATTAAGTGTACCAAGACGAGAAGCAGCATTCTTTTGTAT[G/A]
TGCCAGCGAGAGATGCGATGGCATGTATTTGGAAATACTTCCTCAATTGCCTTTGACATAACTTGATCTTGATTGGTAAAAATAGAGCGAGGATGCCGAT

Reverse complement sequence

ATCGGCATCCTCGCTCTATTTTTACCAATCAAGATCAAGTTATGTCAAAGGCAATTGAGGAAGTATTTCCAAATACATGCCATCGCATCTCTCGCTGGCA[C/T]
ATACAAAAGAATGCTGCTTCTCGTCTTGGTACACTTAATGGTTCCAAAGCATTTAATAAGCTGTTCACCAAGTGTATGCAGGGATGTGACTCAGAAGCTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.20%	2.70%	0.04%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.00%	0.00%	NA
All Japonica	1512	93.30%	6.50%	0.13%	0.00%	NA
Aus	269	95.90%	4.10%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	98.80%	1.00%	0.13%	0.00%	NA
Tropical Japonica	504	93.80%	6.20%	0.00%	0.00%	NA
Japonica Intermediate	241	74.70%	24.90%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	0.00%	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
vg0220739288	G -> A	LOC_Os02g34590.1	synonymous_variant ; p.His377His; LOW	synonymous_codon	Average:51.122; most accessible tissue: Callus, score: 83.375	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220739288	NA	3.83E-06	mr1098_2	Jap_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
vg0220739288	NA	3.39E-07	mr1851_2	Jap_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