Search for Variation information by Variation ID:

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

Detailed information for vg1212815464:

Variant ID: vg1212815464 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 12815464
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: 272. )

Flanking Sequence (100 bp) in Reference Genome:

TGCATTTGAGAAGTATCCCGTTTGGCGCCTTCTTGTACAGATCGTTACCGATCATACAATAAATCTTGGCTTGTCGGGTTATCTTCTCAGCTACTGCATC[G/A]
TCCTCGGGCAACTTGTCACTACTTAGGAACTTGATGAGCGGGGTCCGCCAGTCGTCTGTGGTCTCGATGTCGGCAACGACGTGTTCTGCCCCTAGAGCCC

Reverse complement sequence

GGGCTCTAGGGGCAGAACACGTCGTTGCCGACATCGAGACCACAGACGACTGGCGGACCCCGCTCATCAAGTTCCTAAGTAGTGACAAGTTGCCCGAGGA[C/T]
GATGCAGTAGCTGAGAAGATAACCCGACAAGCCAAGATTTATTGTATGATCGGTAACGATCTGTACAAGAAGGCGCCAAACGGGATACTTCTCAAATGCA

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	92.40%	7.20%	0.38%	0.00%	NA
All Indica	2759	96.70%	3.10%	0.18%	0.00%	NA
All Japonica	1512	88.00%	11.80%	0.13%	0.00%	NA
Aus	269	89.20%	8.60%	2.23%	0.00%	NA
Indica I	595	93.80%	5.70%	0.50%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	97.00%	2.80%	0.11%	0.00%	NA
Indica Intermediate	786	96.90%	2.90%	0.13%	0.00%	NA
Temperate Japonica	767	96.50%	3.40%	0.13%	0.00%	NA
Tropical Japonica	504	85.70%	14.30%	0.00%	0.00%	NA
Japonica Intermediate	241	66.00%	33.60%	0.41%	0.00%	NA
VI/Aromatic	96	50.00%	46.90%	3.12%	0.00%	NA
Intermediate	90	87.80%	10.00%	2.22%	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
vg1212815464	G -> A	LOC_Os12g22700.1	synonymous_variant ; p.Asp205Asp; LOW	synonymous_codon	Average:56.71; most accessible tissue: Zhenshan97 young leaf, score: 80.589	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1212815464	NA	1.36E-06	mr1206	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
vg1212815464	NA	5.35E-06	mr1236	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
vg1212815464	NA	1.20E-06	mr1236	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
vg1212815464	1.85E-06	1.84E-06	mr1597	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
vg1212815464	NA	4.24E-07	mr1558_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