Search for Variation information by Variation ID:

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

Detailed information for vg1223300444:

Variant ID: vg1223300444 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23300444
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGATACTACTCCTATTCGATAGTACTCCCTCCGAAAAAAAGAAAAAAAATAACCTAGCTAAACATAGGTTGAGTTTTTTTAGACGAAAGCAGTGGGTCG[G/A]
AATTTAATGGATGTGTTAGGATTTTGAGTTAGACAGAGTAAGCTACTACTACTCAGTAAGAATTTGGAATATCAATTTCAATATATGACTACATGTTTTT

Reverse complement sequence

AAAAACATGTAGTCATATATTGAAATTGATATTCCAAATTCTTACTGAGTAGTAGTAGCTTACTCTGTCTAACTCAAAATCCTAACACATCCATTAAATT[C/T]
CGACCCACTGCTTTCGTCTAAAAAAACTCAACCTATGTTTAGCTAGGTTATTTTTTTTCTTTTTTTCGGAGGGAGTACTATCGAATAGGAGTAGTATCTA

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	96.90%	2.10%	1.04%	0.00%	NA
All Indica	2759	97.40%	1.20%	1.45%	0.00%	NA
All Japonica	1512	95.20%	4.30%	0.53%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	98.70%	0.80%	0.50%	0.00%	NA
Indica II	465	93.80%	2.40%	3.87%	0.00%	NA
Indica III	913	98.90%	0.80%	0.33%	0.00%	NA
Indica Intermediate	786	96.80%	1.10%	2.04%	0.00%	NA
Temperate Japonica	767	93.20%	6.00%	0.78%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	91.30%	7.90%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg1223300444	G -> A	LOC_Os12g37910.2	upstream_gene_variant ; 1260.0bp to feature; MODIFIER	silent_mutation	Average:90.301; most accessible tissue: Callus, score: 96.949	N	N	N	N
vg1223300444	G -> A	LOC_Os12g37910.1	upstream_gene_variant ; 1260.0bp to feature; MODIFIER	silent_mutation	Average:90.301; most accessible tissue: Callus, score: 96.949	N	N	N	N
vg1223300444	G -> A	LOC_Os12g37920.1	downstream_gene_variant ; 2242.0bp to feature; MODIFIER	silent_mutation	Average:90.301; most accessible tissue: Callus, score: 96.949	N	N	N	N
vg1223300444	G -> A	LOC_Os12g37910-LOC_Os12g37920	intergenic_region ; MODIFIER	silent_mutation	Average:90.301; most accessible tissue: Callus, score: 96.949	N	N	N	N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg1223300444	G	A	-0.09	-0.04	-0.01	-0.03	-0.06	-0.08

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223300444	NA	3.42E-09	mr1498	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
vg1223300444	NA	5.02E-09	mr1769	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
vg1223300444	NA	1.85E-06	mr1925	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
vg1223300444	NA	4.33E-10	mr1951	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
vg1223300444	NA	1.26E-09	mr1951	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
vg1223300444	3.39E-06	3.39E-06	mr1228_2	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
vg1223300444	NA	2.82E-08	mr1498_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
vg1223300444	NA	1.06E-07	mr1498_2	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
vg1223300444	NA	2.31E-06	mr1552_2	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
vg1223300444	NA	1.36E-09	mr1769_2	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
vg1223300444	NA	1.07E-08	mr1951_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
vg1223300444	NA	5.87E-10	mr1951_2	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