Search for Variation information by Variation ID:

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

Detailed information for vg1217860963:

Variant ID: vg1217860963 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17860963
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.02, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

GTATCGAACCGGCCACCGCTAAATGGCCGGATCGATCGAAATTCTAGTCCTATGCTCACGGTGGAACGCTCAACCCAGTTGATGGCTCCCTTGTCTTCAG[C/T]
GATCAGATACGCGAGGCTGCGAGTCGATTAACGGACGCAGTGGAAGCCTCTTCTCAGGGCACGTTCCGACCCGACAGAGAGAAGGACGAGGAGCAAGAGA

Reverse complement sequence

TCTCTTGCTCCTCGTCCTTCTCTCTGTCGGGTCGGAACGTGCCCTGAGAAGAGGCTTCCACTGCGTCCGTTAATCGACTCGCAGCCTCGCGTATCTGATC[G/A]
CTGAAGACAAGGGAGCCATCAACTGGGTTGAGCGTTCCACCGTGAGCATAGGACTAGAATTTCGATCGATCCGGCCATTTAGCGGTGGCCGGTTCGATAC

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	58.50%	10.90%	1.50%	29.07%	NA
All Indica	2759	50.30%	17.40%	1.85%	30.41%	NA
All Japonica	1512	75.60%	0.30%	0.99%	23.08%	NA
Aus	269	46.80%	7.40%	0.37%	45.35%	NA
Indica I	595	83.90%	7.90%	0.00%	8.24%	NA
Indica II	465	46.00%	11.60%	4.30%	38.06%	NA
Indica III	913	31.20%	24.80%	2.08%	41.95%	NA
Indica Intermediate	786	49.60%	19.60%	1.53%	29.26%	NA
Temperate Japonica	767	97.70%	0.10%	0.00%	2.22%	NA
Tropical Japonica	504	48.80%	0.60%	2.18%	48.41%	NA
Japonica Intermediate	241	61.40%	0.40%	1.66%	36.51%	NA
VI/Aromatic	96	46.90%	2.10%	1.04%	50.00%	NA
Intermediate	90	71.10%	7.80%	3.33%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217860963	C -> DEL	N	N	silent_mutation	Average:22.382; most accessible tissue: Zhenshan97 flag leaf, score: 62.519	N	N	N	N
vg1217860963	C -> T	LOC_Os12g29874.1	upstream_gene_variant ; 3192.0bp to feature; MODIFIER	silent_mutation	Average:22.382; most accessible tissue: Zhenshan97 flag leaf, score: 62.519	N	N	N	N
vg1217860963	C -> T	LOC_Os12g29860.1	intron_variant ; MODIFIER	silent_mutation	Average:22.382; most accessible tissue: Zhenshan97 flag leaf, score: 62.519	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217860963	NA	5.15E-06	mr1216	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
vg1217860963	4.01E-06	4.01E-06	mr1321	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
vg1217860963	6.37E-07	6.37E-07	mr1323	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
vg1217860963	NA	1.40E-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
vg1217860963	NA	9.50E-07	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
vg1217860963	2.75E-06	2.75E-06	mr1770	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
vg1217860963	NA	9.00E-06	mr1879	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