Search for Variation information by Variation ID:

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

Detailed information for vg0512814053:

Variant ID: vg0512814053 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 12814053
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

TGGGAACTGAAGCTGATCCAAATGGGGAATATAGACAAGAATCTGGATTGCTGAAGTACAAAGGGAGGATATATGTTGGCCAGGGCACTAACATCAGAAC[C/T]
GAACTGTTGAGGGCATGTCATGCATCCTCTTTTGGTGGTCACTCTAGTATGAGAGCAACTTACCACAGAATCAAACTGTTGTTTTACTGGCCAAGACTTA

Reverse complement sequence

TAAGTCTTGGCCAGTAAAACAACAGTTTGATTCTGTGGTAAGTTGCTCTCATACTAGAGTGACCACCAAAAGAGGATGCATGACATGCCCTCAACAGTTC[G/A]
GTTCTGATGTTAGTGCCCTGGCCAACATATATCCTCCCTTTGTACTTCAGCAATCCAGATTCTTGTCTATATTCCCCATTTGGATCAGCTTCAGTTCCCA

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	64.10%	30.10%	4.38%	1.42%	NA
All Indica	2759	77.30%	15.70%	4.57%	2.43%	NA
All Japonica	1512	46.30%	49.10%	4.63%	0.00%	NA
Aus	269	19.00%	80.30%	0.74%	0.00%	NA
Indica I	595	72.10%	9.90%	10.25%	7.73%	NA
Indica II	465	86.20%	6.50%	6.88%	0.43%	NA
Indica III	913	75.60%	24.20%	0.11%	0.11%	NA
Indica Intermediate	786	77.90%	15.80%	4.07%	2.29%	NA
Temperate Japonica	767	14.00%	81.60%	4.43%	0.00%	NA
Tropical Japonica	504	87.30%	9.50%	3.17%	0.00%	NA
Japonica Intermediate	241	63.50%	28.20%	8.30%	0.00%	NA
VI/Aromatic	96	93.80%	5.20%	1.04%	0.00%	NA
Intermediate	90	64.40%	26.70%	8.89%	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
vg0512814053	C -> T	LOC_Os05g22560.1	synonymous_variant ; p.Thr420Thr; LOW	synonymous_codon	Average:52.089; most accessible tissue: Zhenshan97 young leaf, score: 85.886	N	N	N	N
vg0512814053	C -> DEL	LOC_Os05g22560.1	N	frameshift_variant	Average:52.089; most accessible tissue: Zhenshan97 young leaf, score: 85.886	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0512814053	2.25E-06	3.48E-13	mr1552	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
vg0512814053	NA	6.61E-07	mr1657	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
vg0512814053	NA	1.89E-06	mr1582_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
vg0512814053	NA	7.68E-18	mr1807_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