Search for Variation information by Variation ID:

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

Detailed information for vg0212395942:

Variant ID: vg0212395942 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 12395942
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

CCCCATTCATGATGAGCATATTAGTCATCTAGCGTTGTCCTTAATCCACCTTTAACTAACACACTACTACAGAAAAGAAGATAGGTGTCGGTTGGGAACC[G/A]
GTCATAGGTGCTGAATTTTCCAACCGACATGTAGTGAGGTCTCAAATGTGTCAGTTTAAAAACCTACAAATAACAAAAAAAAAGGAAAAAAAAAGCTGGC

Reverse complement sequence

GCCAGCTTTTTTTTTCCTTTTTTTTTGTTATTTGTAGGTTTTTAAACTGACACATTTGAGACCTCACTACATGTCGGTTGGAAAATTCAGCACCTATGAC[C/T]
GGTTCCCAACCGACACCTATCTTCTTTTCTGTAGTAGTGTGTTAGTTAAAGGTGGATTAAGGACAACGCTAGATGACTAATATGCTCATCATGAATGGGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.60%	30.60%	0.83%	0.00%	NA
All Indica	2759	96.60%	3.00%	0.33%	0.00%	NA
All Japonica	1512	22.30%	76.10%	1.59%	0.00%	NA
Aus	269	68.80%	31.20%	0.00%	0.00%	NA
Indica I	595	99.20%	0.70%	0.17%	0.00%	NA
Indica II	465	97.20%	2.60%	0.22%	0.00%	NA
Indica III	913	97.60%	2.10%	0.33%	0.00%	NA
Indica Intermediate	786	93.30%	6.20%	0.51%	0.00%	NA
Temperate Japonica	767	4.20%	95.40%	0.39%	0.00%	NA
Tropical Japonica	504	52.20%	44.20%	3.57%	0.00%	NA
Japonica Intermediate	241	17.40%	81.30%	1.24%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	55.60%	37.80%	6.67%	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
vg0212395942	G -> A	LOC_Os02g20950.1	downstream_gene_variant ; 1699.0bp to feature; MODIFIER	silent_mutation	Average:68.425; most accessible tissue: Minghui63 young leaf, score: 80.234	N	N	N	N
vg0212395942	G -> A	LOC_Os02g20960.1	downstream_gene_variant ; 267.0bp to feature; MODIFIER	silent_mutation	Average:68.425; most accessible tissue: Minghui63 young leaf, score: 80.234	N	N	N	N
vg0212395942	G -> A	LOC_Os02g20970.1	downstream_gene_variant ; 2479.0bp to feature; MODIFIER	silent_mutation	Average:68.425; most accessible tissue: Minghui63 young leaf, score: 80.234	N	N	N	N
vg0212395942	G -> A	LOC_Os02g20950-LOC_Os02g20960	intergenic_region ; MODIFIER	silent_mutation	Average:68.425; most accessible tissue: Minghui63 young leaf, score: 80.234	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0212395942	NA	3.54E-20	mr1422	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
vg0212395942	NA	1.27E-08	mr1422	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
vg0212395942	NA	3.31E-06	mr1583	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
vg0212395942	NA	2.45E-07	mr1622	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
vg0212395942	NA	1.87E-06	mr1850	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
vg0212395942	9.75E-07	NA	mr1042_2	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
vg0212395942	NA	2.58E-07	mr1042_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
vg0212395942	NA	5.06E-07	mr1047_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
vg0212395942	NA	5.27E-09	mr1235_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
vg0212395942	NA	2.43E-07	mr1257_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
vg0212395942	NA	6.05E-06	mr1319_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
vg0212395942	NA	6.93E-08	mr1423_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
vg0212395942	NA	6.32E-07	mr1495_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
vg0212395942	NA	2.59E-09	mr1543_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
vg0212395942	NA	1.33E-09	mr1624_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
vg0212395942	NA	1.29E-15	mr1720_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
vg0212395942	5.39E-06	3.93E-10	mr1742_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
vg0212395942	1.78E-09	NA	mr1871_2	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
vg0212395942	1.09E-06	3.34E-08	mr1871_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