Search for Variation information by Variation ID:

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

Detailed information for vg1207220741:

Variant ID: vg1207220741 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7220741
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

AATAGTTAATTTCCTTAATTCTGTCATGATCTGATGCAGCTTCCAAAATTCCCCAAGTCTGAAAGAGAGCTCAATGATACATCCATTCAGAACATTCAGG[C/T]
GGACATGTGCTACTTCATCCACCGTGAGTGCGCACATCAGCCTGGGCGGTTTTTCGACAACGAAGGAGTCTTAGCCCTGCCGGAGAACGAATCCCTGTCT

Reverse complement sequence

AGACAGGGATTCGTTCTCCGGCAGGGCTAAGACTCCTTCGTTGTCGAAAAACCGCCCAGGCTGATGTGCGCACTCACGGTGGATGAAGTAGCACATGTCC[G/A]
CCTGAATGTTCTGAATGGATGTATCATTGAGCTCTCTTTCAGACTTGGGGAATTTTGGAAGCTGCATCAGATCATGACAGAATTAAGGAAATTAACTATT

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	88.30%	11.70%	0.04%	0.00%	NA
All Indica	2759	87.00%	12.90%	0.07%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	46.80%	53.20%	0.00%	0.00%	NA
Indica I	595	89.20%	10.80%	0.00%	0.00%	NA
Indica II	465	90.50%	9.50%	0.00%	0.00%	NA
Indica III	913	88.20%	11.60%	0.22%	0.00%	NA
Indica Intermediate	786	81.80%	18.20%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	50.00%	50.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg1207220741	C -> T	LOC_Os12g13020.1	missense_variant ; p.Ala852Val; MODERATE	nonsynonymous_codon ; A852V	Average:17.82; most accessible tissue: Minghui63 young leaf, score: 23.613	benign	0.181	TOLERATED	0.48

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207220741	3.20E-06	7.95E-06	mr1324	Ind_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
vg1207220741	6.53E-06	NA	mr1335	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
vg1207220741	2.10E-06	4.55E-06	mr1335	Ind_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
vg1207220741	NA	2.95E-07	mr1347	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
vg1207220741	9.83E-06	8.89E-06	mr1482	Ind_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
vg1207220741	2.70E-06	2.53E-06	mr1590	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
vg1207220741	6.01E-06	NA	mr1660	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
vg1207220741	5.03E-06	NA	mr1660	Ind_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
vg1207220741	NA	6.79E-07	mr1705	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
vg1207220741	4.57E-07	4.40E-09	mr1815	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
vg1207220741	4.94E-06	NA	mr1815	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
vg1207220741	8.74E-07	9.95E-06	mr1964	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